Methods for designing and synthesizing directed sequence polymer compositions via the directed expansion of epitope permeability

ABSTRACT

The instant invention comprises a process for the solid phase synthesis of directed epitope peptide mixtures useful in the modulation of unwanted immune responses, such process defined by a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known epitope. The resulting composition is a mixture of related peptides for therapeutic use.

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application 60/792,085, filed Apr. 13, 2006.

FIELD OF INVENTION

This application provides methods of making improved compositions of immunomodulatory peptide mixtures and provides methods of modulating unwanted immune responses.

BACKGROUND OF THE INVENTION

Immunomodulation.

Many disease conditions are, at least in part, a result of an unwanted or excessive immune response within an organism. The rejection of a transplanted organ is axiomatic example of an unwanted immune response. The rejection of the graft is emblematic of a condition in which an organism's inability to control an immune response results in a pathology. In organ transplantation, the unwanted immune response that results in graft rejection is triggered by: (1) “direct recognition,” where the T cells of the graft recipient recognize foreign major histocompatibility complex (“MHC”) molecules on the graft tissue, already presenting some peptides, via their T-cell receptor (“TCR”) directly, or “indirect recognition,” where the recipient T cells recognize the antigenic determinants derived from the graft after the determinants are processed and presented by recipient MHC; (2) the generation of antibodies directed against the graft, more specifically, the human leukocyte antigens (“HLA”) molecules present on the cells of the graft tissue, caused by the exposure of the recipient to the graft; and (3) binding of preformed anti-graft antibodies in the circulation of the recipient to the graft. Studies have shown that these immune responses are directed to three types of donor derived antigens: MHC (through direct or indirect recognition), minor histocompatibility antigens (“mH”), and organ derived antigens.

Successful transplantation depends on preventing the unwanted immune responses, inducing sustained chimerism. Sustained chimerism is a phenomenon in which the recipient develops tolerance for a foreign graft, enabling the grafted tissue to survive in the recipient without being subjected to immune responses. Under experimental conditions, sustained chimerism can be induced by peptides that are closely related to those that stimulate graft-rejecting immune responses, albeit for short periods of time. (B. Murphy et al., J. Am. Soc. Nephrol., 2003, 14:1053-1065; C. LeGuern, Trends Immunol., 2003, 24:633-638). The difficulty lies with the likelihood of the broadening of the offending epitopes via the process of epitope spreading (N. Suciu-Foca et al., Immunol. Rev., 1998, 164:241).

Transplant physicians have long recognized the need both to inhibit the immune response generated by the presence of what the recipient's immune system views as foreign, without also compromising the patient's ability to fight opportunistic infection. Currently, transplantation patients are often treated with immunosuppressive therapies that depress the overall immune response and reactivity in a patient. Immunosuppressive therapies attempt to attenuate the reaction of the body to an already-triggered immune response, and are accompanied by numerous undesirable side effects. Because of the significant undesirable side effects, a single immunosuppressant cannot be used continuously to treat a transplant recipient, and a course of treatment comprises using one immunosuppressant having one set of side effect, changing to second immunosuppressant with a different set of side effect, and to third, and so on, to limit the exposure of the recipient to each immunosuppressant and its side effects. For example, steroids such as prednisone or methylprednisone are powerful immunosuppressants but can induce cataracts, hyperglycemia, hirstutism, bruising, acne, bone growth suppression, and ulcerative oesophagitis. Long term use of steroids has also been associated with bone loss. Cyclosporin A (CsA), a widely used immunosuppressant, is nephrotoxic, and often replaced with tacrolimus (TAC) after a period of treatment. For the treatment of non-acute rejection, azathioprine is used, the side effect of which include leucopenia, anemia, fever, chills, nausea and vomiting. Regardless of what immunosuppressant is used, one of the most substantial side effects related to longer term treatment with immunosuppressives in addition to the general compromise of the immune system leaving the patient vulnerable to any type of infections, is the generation of transplant related malignancies such as Kaposi's sarcoma. There is a strong desire on the part of physician and patient to decrease or cease the use of these current front line therapies. (Pharmacotherapy: A pathophysiologic Approach, Fifth Edition. 2002, McGraw Hill.) It would be difficult to state that they have met the clinical goal of sustained chimerism without ongoing immunosuppressive therapy.

Immunomodulation, in contrast to immunosuppression, targets the cause of unwanted immune responses. Immunomodulation can be attempted in an antigen/epitope non-specific fashion by targeting the body's mechanism for immunity, or in an antigen/epitope specific manner. As an example of antigen/epitope non-specific treatment, therapies directly targeted at controlling T lymphocytes or their functions have been developed using biotechnological tools. The therapeutic agents useful for such treatment include Muromonab-CD3 (OKT3), antilymphocyte globulin (ALG), antithymocyte globulin (ATG), or interleukin-2 receptor monoclonal antibody (“mAb”) daclizumab or basiliximab. Other agents include soluble CTLA-4, an anti-CD154 mAb; anti-CD11a; a humanized mAb which inhibits VLA-4; anti-CD2, 3, or 4 antibodies; and anti-CD152 antibodies (J. B. Matthews et al., Amer. J. Transplantation, 2003, 3: 794-80). While all of these therapeutic agents may induce a state of non-responsiveness of the recipient's immune system to the transplanted tissue with a reduction in side effects, as compared to e.g. prednisone, the therapies still do not meet the clinical goal of sustained chimerism without ongoing immunosuppressive therapy, except for limited reports, such as immunosuppressive withdrawal after combination therapy of total lymphoid irradiation followed by ATG administration (S. Strober et al., Transplantation, 2004 Mar. 27; 77(6): 932-936). Further, these therapies also suffer from the unattractive side effects of compromised overall immune function.

In contrast to the antigen non-specific immunomodulatory approach, the immune system can also be retuned, or modulated in an antigen/epitope specific manner. Such a type of immunomodulation is the process of increasing or decreasing the immune system's ability to mount a response against a particular antigenic determinant through either the TCR's recognition of complexes formed by MHC and antigens, or through the B cell receptor's (“BCR”) recognition of the epitope itself. Because of the specificity of the process toward a particular antigenic determinant and not toward the immune system as a whole, antigen specific immunomodulation has advantages such as fewer undesirable side effects compared to current treatment modalities such as immunosuppressive therapies, which affects the overall immune system.

Antigenic determinant-specific immunomodulatory treatments can help establish such sustained chimerism by inducing donor-specific tolerance in host T lymphocytes. Immunomodulation of the reaction toward any and all of these antigens help attenuate or alleviate graft rejection and establish sustained chimerism. Studies indicate that one mechanism of action of immunomodulation by certain immunomodulatory peptides may be through their binding to T cells that would otherwise bind to the donor-derived antigens and resulting in differential activation of T cell functions. This mechanism has been suggested to be centrally induced tolerance involving the thymus (G. Benichou et al. Immunol. Today, 1997, 18(2):67-72). The demonstration of achieving sustained chimerism without immunosuppressive treatment via induction of donor-specific tolerance in host T lymphocytes through immunomodulation was performed by a group of investigators who, using mice, induced tolerance to the subsequent graft by intrathymic injection of a series of determinants from 3M KCl-extracted donor MHC-derived peptides. Two doses of anti-T cell antibody were given first to eliminate circulating T cells. Then eight peptide sequences extracted from the donor MHC were delivered in combination. The treated mice tolerated subsequent transplants. As a control, the investigators performed thymectomy, which caused graft rejection. The study is an example of importance of centrally-induced tolerance (T. Hamashima et al., Transplantation, 1994 Jul. 15; 58(1):105-7). Thus, designing appropriate peptides similar to T cell-stimulating antigens that bind to the T cells is beneficial to achieving sustained chimerism.

However, the difficulty lies with the likelihood of the broadening of the offending epitopes via the process of epitope spreading. (N. Suciu-Foca et al., Immunol. Rev. 1998, 164:241). Thus, in transplantation, the axiomatic example where certain immune response is unwanted, it is clear that, in the absence of the ability to modulate the relevant antigenic determinants over time, the only alternatives are non-specific immunomodulatory, or immunosuppressive therapies.

Other examples of unwanted immune responses are autoimmune diseases. One important contextual difference between autoimmune diseases and transplantation rejection is that the offending antigenic determinant(s) is/are generally more restricted and definable. While the trigger of an autoimmune disease is undefined and may be dictated by pre-existing and/or environmental factors, the direct causes of the pathological condition have been identified in many autoimmune diseases. An autoimmune disease results from an inappropriate immune response directed against a self antigen (an autoantigen), which is a deviation from the normal state of self-tolerance. Self-tolerance arises when the generation of T cells and B cells capable of reacting against autoantigens has been prevented or altered centrally by events that occur either in their early development or after maturation in the periphery. The cell surface proteins that play a central role in regulation of immune responses through their ability to bind and present processed peptides to T cells via the T cell receptor (TCR) are class I and class II MHC (J. B. Rothbard et al., Annu. Rev. Immunol., 1991, 9:527).

Thus, an attractive point of intervention for the amelioration of an autoimmune response is via the set of lymphocyte surface protein MHC molecules for example, HLA-DR, -DQ and -DP, themselves or in combination with the peptides they present. Different HLA alleles generate a diversity of responses via antigenic-determinant specificities by variable affinities for protein fragments found in the extra- and intra-cellular milieu because of differences in the amino acids which are directly involved in the binding of the peptides. There are large numbers of alternative or allelic forms within a mammalian population, but only a few of these allelic forms are associated with disease-related antigenic determinants. It is well understood to one with ordinary skill in the art the genomes of subjects affected with certain autoimmune diseases, for example MS and RA, are more likely to carry one or more such characteristic MHC class II alleles, to which that disease is linked. For example, HLA-DR2 (DRB1*1501) is associated with multiple sclerosis and HLA-DR1 (DRBI*0101) or HLA-DR4 (DRB1*0401) are associated with rheumatoid arthritis.

The disease-related antigenic determinants derive from proteins which have been described as being simply associated with an autoimmune response, or as being part of the pathogenesis of the disease process itself. There are highly conserved sequences within HLA that may play a role in either the generation or regulation of immunologic tolerance when processed into peptides and presented by intact HLA (reviewed in B. Murphy and A. M. Krensky, J. Am. Soc. Nephroi., 1999, 10:1346-55). A. Snijders et al. discuss one particular sequence (KDILEDERAAVDTYC) (SEQ ID NO: 206) presented by HLA-DRB1 as being protective against rheumatoid arthritis, with the most relevant portion of the peptide being DERAA (SEQ ID NO: 207) (J. Immunol., 2001, 166:4987-93), while others have promoted what is known as the ‘shared epitope hypothesis’ (P. K. Gregersen et al., Arthritis Rheumatism 1987 November; 30(11):1205-13) where those individuals that carry HLA-DRB1 alleles having the sequence QKRAA (SEQ ID NO: 208) are predisposed to rheumatoid arthritis. Other investigators have demonstrated that heat shock proteins (hsp) and the peptides derived from them can have immunomodulatory properties (S. M. Anderton et al., J. Exp. Med., 1995, 181:943-952; J. A. van Roon et al., J. Clin. Invest., 1997, 100:459-063). One peptide in particular, dubbed p277, derives from hsp60, VLGGGVALLRVIPALDSLTPANED (SEQ ID NO: 147), has demonstrated apparent activity in the context of Type I diabetes (I. Raz et al., Lancet, 2001, 358:1749-52). Further sources of epitope sequence may be derived from a pathogen-derived mimic of a sequence within mammalian MHC proteins such as the DNAjP1 peptide, or related peptides (QKRAAYDQYGHAAFE (SEQ ID NO: 209); Proc. Nat. Acad. Sci. USA, 101:4228-33; U.S. Pat. No. 6,989,146). Other proteins and the peptides that derive from them having disease association are: glutamate decarboxylase (GAD) with diabetes (M. A. Atkinson et al. J. Clin. Invest., 1994, 94:2125-29; D. B. Wilson J. Autoimmun., 2003, 20:199-201); myelin associated proteins such as myelin basic protein (MBP), myelin-associated glycoprotein (MAG), proteolipid protein (PLP), and myelin oligodendrite glycoprotein (MOG) with multiple sclerosis (reviewed in P. Fontoura et al., Int. Rev. Immunol., 2005, 24:415-46); Ro60, SmD and other ribonucleoprotein antigens with lupus (R. Pal, et al., J. Immunol., 2005, 175:7669-77; Seshmukh et al., J. Immunol., 2000, 164:6655-61; R. R. Singh, Mol. Immunol., 2004, 40:1137-45); or the acetylcholine receptor (AChR) with myasthenia gravis (MG) (S. L. Kirshner, et al. Scand. J. Immunol., 1996, 44:512-21); or desmoglein 3 (DsG3) with pemphigus vulgaris (PV) (Wucherpfennig et al., Proc. Nat. Acad. Sci. USA, 1995, 92:11935-9; Lin et al., J. Clin. Invest., 1997, 99:31-40; Veldman et al., J. Immunol., 2004 172:3883-92; Angelini et al., J. Translational Med., 2006, 4:43; U.S. Pat. No. 5,874,531; U.S. Pat. No. 7,084,247).

Despite the attraction of using HLA alleles and their associated antigenic determinants that have been linked to many autoimmune diseases as a point of intervention, therapeutic agents based on this knowledge have not been developed fully. Instead, a number of immunomodulatory therapeutic agents that are not specific to any particular antigenic determinant have been developed and being used to treat autoimmune diseases, including general anti-inflammatory drugs such as cyclooxygenase-2 (COX-2) inhibitors that can prevent formation of low molecular weight inflammatory compounds; inhibitors of a protein mediator of inflammation such as tumor necrosis factor (TNF), such as an anti-TNF specific monoclonal antibody or antibody fragment, or a soluble form of the TNF receptor that sequester TNF; and agents that target a protein on the surface of a T cell and generally prevent interaction with an antigen presenting cell (APC), for example by inhibiting the CD4 receptor or the cell adhesion receptor ICAM-1. However, these types of antigenic-determinant non-specific immunomodulatory therapeutic agents have residual immunosuppressive-like side-effects which diminish their attractiveness as chronic first line therapies. Additionally, compositions having natural folded proteins (such as antibodies) as therapeutic agents can encounter problems in production, formulation, storage, and delivery. Several of these problems necessitate delivery to the patient in a hospital setting.

Strategy for Creating Synthetic Therapeutic Peptides

Drug discovery can be generalized into two major elements, lead generation and lead optimization. The development and exploitation of combinatorial chemistry (CC) has seen the divergence of the uses of rational design versus random generation on a very fundamental level. On one side we find the use of CC to assist a researcher in the rational design of molecules. An example of which can be seen in the discovery of structure/activity relationships (SAR) between two or more active molecules of therapeutic interest. On the other side we find researchers using CC to define for them the design of new molecules discovered based on a specific activity. An example of which would be the generation of random libraries used in lead generation, whereby the lead is singled out and further optimized.

The level of expertise in the state of the art of combinatorial chemistry as applied to the synthesis of peptide libraries has risen, producing highly reliable and pure mixtures of peptides of great diversity. The use of these diverse peptide libraries has focused on lead generation and optimization. This strategy entails screening the vast numbers of individual peptide sequences in the library against a target of interest with the intention of defining a single, or limited set of peptides which demonstrate a particular activity. That single peptide, or the limited set of peptides, then become candidates which are modified to increase activity against the target. This process is schematically represented in FIG. 1A.

The challenge for practitioners in this art has been to deconvolute, or accurately define the single or limited set of peptides that were responsible for the observed activity. The difficulties associated with deconvolution have spawned great efforts on the part of practitioners to create synthesis methods which inherently increase the resolution of individual peptides, as well as the identity of individual amino acids within peptides.

In order to efficiently identify the target peptide from myriad of candidates presented by a library created by combinatorial chemistry, a variety of synthesis methods and approaches have been developed. These synthesis methods aim to provide a large number of candidates, and yet when a positive result is obtained, to quickly determine the identity of the peptide without having to laboriously isolate the positive species from the rest. The effort put forth by practitioners in this art in this regard is an indication of the industry-wide vision of the method's ultimate utility, which is to allow the random complexity of these libraries perform the screening process for the desired activity.

Examples of the resulting evolution of subtypes of combinatorial methods include: multiple synthesis, iterative synthesis, positional scanning, and one-compound-one-bead post assay identification design.

Multiple synthesis” provides for any method whereby distinct compounds are synthesized simultaneously to create a library of isolated compounds. The identity of these compounds would be known from the rules of the synthesis. H. M. Greysen et al., Proc. Nat. Acad. Sci. USA, 1984, 81:3998, used the multiple synthesis method to identify peptides that bound to an antibody raised against VPI protein of foot-and-mouth disease virus. The investigators identified GDLQVL (SEQ ID NO: 210) as the epitope recognized by the antibody. In this case the authors synthesized 108 overlapping peptides representing the VPI sequence on pins in a 96-well microplate array.

“Iterative synthesis/screening” involves methods of peptide synthesis which allow for a determination of the identity of individual residues within peptide sequences. An example of iterative synthesis can be seen in R. A. Houghten et al., Nature, 1991, 354:84-86, also to determine antibody binding epitopes. These investigators identified the sequence YPYDVPDYASLRS (SEQ ID NO: 211) using an ELISA type assay format. The first library consisted of 324 pools of peptides with the first two residues fixed, which peptides can be shown as O₁O₂XXXX, wherein O1 and O2 are the fixed residues and X is randomly selected. The process identified DV as the fix residues. The next step was to do the same for position three, by synthesizing peptides that can be shown as DV O₁XXX, wherein O1 again is a fixed residue. When the process identified which residue at the third position would elicit the desired binding, that residue was adopted as the unchanging third residue, and the fourth position was explored in a similar manner. The process continued until the native sequence DVPDYA (SEQ ID NO: 212) was identified.

“Positional scanning” is a synthesis method producing complex mixtures of peptides that allows for the determination of the activity of each individual peptide. Based on the screening results, the derived peptide can then be separately synthesized for optimization. As seen in C. Pinilla et al., Biochem J., 1994, 301:847-853, positional scanning libraries were used to identify decapeptides which bound the same YPYDVPDYASLRS-binding (SEQ ID NO: 211) antibody. In this case ten different libraries each containing 20 pools with a defined amino acid at each of the ten positions in the peptide. Fifteen peptides were identified.

Each of the above methods were also employed to identify enzyme substrates (J. H. Till et al., J. Biol. Chem., 1994, 269:7423-7428, J. Wu et al, Biochemistry, 1994, 33:14825-14833, W. Tegge et al., Biochemistry, 1995, 34:10569-10577), or enzyme inhibitors (M. Bastos et al., Proc. Nat. Acad. Sci. USA, 1995, 92:6738-6742, Meldal et al., Proc. Nat. Acad. Sci. USA, 1994, 91:3314-3318), R. A. Owens et al., Biomed Biophys. Res. Commun., 1994, 181:402-408, J. Eichler. et al., Pept. Res., 1994, 7:300-7). These powerful tools allow investigators to rationally design combinatorial peptide libraries to identify a single species which has a desired activity.

As powerful and clear cut the identification of a specific peptide from a combinatorial library may be, it may only serve as a starting point and identification of a lead peptide that is not itself therapeutically useful. The identified epitope may be ignored by the immune system if it resembles a self protein or possibly exacerbate the very condition that the therapy aims to relieve. Such peptide is not directly therapeutically useful. However, one may create, based on such peptide, epitope reactive analogs that would act as modifiers of the unwanted immune response.

One such approach is creation of altered peptide ligands (APL). This approach is schematically represented in FIG. 1B. An APL is defined as an analog peptide which contains a small number of amino acid changes from the native immunogenic peptide ligand. Some of such APLs act as an antagonist to the T cell receptor, blocking the stimulating binding by the antigens causing the unwanted immune effect. Evabold et al., Proc. Nat. Acad. Sci. USA, 1994 Mar. 15; 91(6):2300-4. However, while recognition of the native response may induce an angonist like reaction, an APL might induce a partial agonist response, or induce a state of energy in the reactive T cell population. In discussing APL in the context of allograft rejection therapy, Fairchild et al., Curr. Topics Peptide Protein Res., 2004, 6:237-44, note that an APL acting as an antagonist for one TCR, may become an agonist for another, complicating the rational design of an APL. Compounding the obstacle of the development of APL is the difficulty in translating a response developed in an animal system into human.

Despite these challenges, MPB83-99 (ENPVVHEFKNIVTPRTP) (SEQ ID NO: 213) was made into an APL and placed into limited human trials by replacing the bold and underlined amino acid residues “E”, “N”, “E” and “K,” resulting in a single peptide sequence consisting of AKPVVHLFANIVTPRTP (SEQ ID NO: 214), Kim et al. Clinical Immunology, 2002, 104:105-114. The authors describe the long term immune reactivity against the peptide, but the treatment has been deemed clinically ineffective by evaluation using MRI. Thus an APL, once identified, can be used as a therapeutic agent; however, its effectiveness may be limited in terms of clinical efficacy.

It has been observed for some time that in the course of development of multiple sclerosis, the reactive epitope does not stay constant. That is, the self recognition associated with the development of MS is a developmental process characterized by autoreactive diversity, plasticity, and instability, wherein the target epitope changes over time, typically from one epitope on a myelin proteolipid protein to one overlapping the amino acid residues but shifting by one or few amino acids to either side of the original epitope. The consequence of this phenomenon is that if an immunotherapeutic drug was targeted at the original epitope, over time, it becomes ineffective, not because of resistance to the mechanism of the drug, but simply because the target is no longer valid. J. Clin. Invest., 1997, 99:1682-1690.

A method conceived to make an investigational concept like a mixture of peptides into a drug is peptide dendrimer structures. Peptide dendrimers solve certain manufacturing issue of soluble peptide mixtures, in part by the promise of delivering to a patient a consistent ratio and quantity of each of the peptides in the mixture. This approach is schematically represented in FIG. 1C.

Dendrimers are diverse. They can range in size from 2 kDa to greater than 100 kDa. The design of dendrimers intends to mimic two traits of naturally occurring biological structures: a globular structure and polyvalency. As described in two comprehensive reviews (P. Niederhafier et al., J Peptide Sci. 11:757-788; K. Sadler and J. P. Tam, Rev. Mol. Biotechnol., 2002, 90:195-229), they are complex compounds that contain highly branched components organized in a radial or wedge-like fashion, and are intended to have an extensive three-dimensional structure. They have three distinct structural features: a central core surface functionalities and branching units that link the two. Peptide dendrimers are designed as vehicles for delivery of: RNA and DNA as gene expression therapeutics, biosensor systems as diagnostics, inhibitors of autoimmune diseases or cancer metastasis. The strategy behind each of these applications is to use the globular, polyvalent structure to amplify the ligand:substrate interaction (D. Zanini and R. Roy, J. Org. Chem., 1998, 63:3468-3491; J. Haensler and F. C. Szoka, Bioconjug Chem., 1993, 4:372-379).

Dendrimers have been made using amino, hydroxyl, carboxy, poly(propylenimine), silicone and polyamino amine cores (G. M. Dykes et al., J. Chem. Technol. Biotechnol., 2001, 76:903-918, P. Sadler and J. Jezek, Rev. Mol. Biotechnol., 2002, 80:195-229, and J. P. Tam, Methods Org. Chemistry, 2004, Vol E22d 129-168. Peptide dendrimers can be divided into three types: grafted peptide dendrimers, branching polyamino acids and multiple antigen peptides (MAPs).

The branching strategies in MAPs vary widely. The majority of first generation branches have used lysine. Second generation solid phase synthesis of MAPs has seen an interest in proline. The interest is said to come from both the properties of its secondary amine which decreases the reactivity during production, as well as its role in many cellular functions.

Simple MAPs have been synthesized using solid phase chemistry, with this type of synthesis strategy called divergent. Synthesis methods have been described which involves a two-step iterative reaction sequence producing concentric shells of dendritic beta-alanine units covalently linked in the second step to various functional groups (Kojima et al., Bioconjugate Chem., 2000, 11:910-17). These types of MAPs, which are synthesized using the divergent strategy, by necessity have simple branching schemes with few distinct members, as the purification and characterization are untenable with more complex MAPs. The end-product needs to be purified away from deletion compounds having similar characteristics to the end-product. Purifications have been described using gel filtration chromatography, reverse phase high-performance liquid chromatography (HPLC), or electromigration methods.

For complex MAPs, for example, those having a multiplicity of branching moieties, convergent synthesis is the preferred synthesis strategy. Convergent synthesis can be performed using either fragment condensation or ligation of the pre-purified fragments. There are many types of ligations: natural (true peptide bond created), thiol, hydrazone, or other. MAPs prepared using convergent synthesis strategies are easier to purify, as the end-product will look distinctly different from the reaction byproducts. HPLC was first used to purify convergent MAPs (J. C. Spetzler et al., Int. J. Pept. Protein Res., 1995, 45:78-85).

However, a high cost of manufacturing and the subsequent analytical development precludes this technology from being further currently developed commercially.

All of the above strategies, while recognizing the advantage of variations in the therapeutic peptide compositions, derive from the concept that there is one or more defined peptide sequence evoking a defined immunological response. These strategies have attempted to multiply and diversify modulatory peptides via the introduction of defined, single changes performed one at a time.

An entirely different approach which has evolved alongside the defined sequence peptide immunotherapy approach is the use of limited amino acid diversity, random epitope polymers. Random sequence polymers (RSP) can be described as a random order mixture of amino acid copolymers comprising two or more amino acid residues in various ratios, forming copolymers by random sequence bonding, preferably through peptide bonds, of these amino acid residues, which mixture is useful for invoking or attenuating certain immunological reactions when administered to a mammal. Because of the extensive diversity of the sequence mixture, a large number of therapeutically effective peptide sequences are likely included in the mixture. In addition, because of the additional peptides which may at any given time not be therapeutically effective, but may emerge as effective as the epitope shifting and spreading occurs, the therapeutic composition may remain effective over a time of dosing regimen. This approach is schematically represented in FIG. 1D.

Starting in 1959 (P. H. Maurer et al., J. Immunol., 1959, 83:193-7) to 1988, (J. L. Grun, and P. H. Maurer, Immunogenetics, 1988, 28(1): 61-3) Maurer and colleagues investigated the immune responses to poly glutamic acid and other random sequence polymers such as those consisting of tyrosine, glutamate and alanine (YEA), phenylalanine, glutamate and alanine (FEA), and phenylalanine, glutamate and lysine (FEK). Teitelbaum et al., Eur. J. Immunol., 1971, 1:242-8 was the initial report of work on random copolymer consisting of tyrosine, glutamate, alanine and lysine, that eventually culminated in an FDA approved therapy for multiple sclerosis using COP-1, described below. In 1978, Germain and Benacerraf, J. Exp. Medicine 148:1324-37, investigated suppressor T cell responses to YEA in what was to become Benacerrafs 1980 Nobel winning work on the role of MHC in the immune system and its relevance to alloreactivity (http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html).

Copolymer-1 (also known as Copaxone, glatiramer acetate, COP-1, or YEAK (SEQ ID NO: 217) random copolymer), is used for the treatment of multiple sclerosis. Random copolymers are described in International PCT Publication Nos. WO 00/05250, WO 00/05249; WO 0/59143, WO 0027417, WO 96/32119, WO/2005/085323, in U.S. Patent Publication Nos. 2004/003888, 2002/005546, 2003/0004099, 2003/0064915 and 2002/0037848, in U.S. Pat. Nos. 6,514,938, 5,800,808 and 5,858,964.

SUMMARY OF THE INVENTION

The instant invention comprises a process for the solid phase synthesis of directed epitope peptide mixtures useful in the modulation of unwanted immune responses, such process defined by a set of rules regarding the identity and the frequency of occurrence of amino acids that substitute a base or native amino acid of a known epitope. A method of the instant invention uses a sequence of a known peptide epitope as a starting point. The amino acids that make up the epitope are sequentially modified via the introduction of different, related amino acids defined by a set of rules. The result is a mixture of related peptides useful in and of itself as a therapeutic, which is described herein as a composition comprising “directed-sequence polymers” or “DSP”. Such composition is referred to as a “DSP composition.” The method of synthesizing a DSP composition utilizes and maintains the natural order of amino acid residues of a defined peptide sequence of a specified length. Each amino acid position is subjected to change based on a defined set of rules. In a preferred embodiment the amino acids is substituted according to the methods seen in Table X of Kosiol et al., J Theoretical Biol., 2004, 228:97-106). Alternatively, amino acids can be changed in accordance with the exemplary substitutions described in PCT/US2004/032598, page 10-11. For the solid phase synthesis procedure of the instant invention, the mixture of amino acids for a given position in the peptide is defined by a ratio one to another. Prior to starting the synthesis, such ratio is determined for each position along the peptide. The resulting directed order peptide mixture comprises a multiplicity of related peptide sequences.

The length of a DSP can be one of the original defined sequence peptide or 30 lengths of the original defined sequence peptide. The length of the combined sequence can be between 25 and 300 amino acids.

The percentage of alanine as compared to all of the other amino acids in the DSP combined will always be greater than 10%, and will not exceed 90%. Preferably, the alanine percentage is between 20% and 80%. More preferably the percentage of alanine is between 40% and 75%. The complexity of the mixture is greater than 5×10² different peptides. Preferably the complexity of the mixture is greater than 1×10¹⁰ different peptides. More preferably the complexity of the mixture is greater than 1×10¹⁵ different peptides.

In some embodiments, the base peptide sequence from which the DSP sequences are derived is selected from a group consisting of SEQ ID NO: 1 through 189 and 205 depicted in Table 1.

In other embodiments, such base peptide sequence is an epitope relevant to the pathology of an autoimmune disease selected from the group consisting of multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris. More particularly, the base peptide sequence is a partial sequence of a protein selected from the group consisting of: (a) osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), 2′,3′ cyclic nucleotide 3′-phosphodiesterase; (b) hsp60, hsp70, Ro60, La, SmD, and 70-kDa U1RNP; (c) glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), insulin; (d) acetylcholine receptor (AChR) α-subunit and muscle-specific receptor tyrosine kinase (MuSK); (e) type II collagen; and (f) desmoglein 3 (Dsg3)

One aspect of the present invention is a pharmaceutical composition comprising a DSP composition, optionally as a pharmaceutically acceptable salt. In a preferred embodiment, such pharmaceutical composition comprising a DSP composition, when administered to a subject, causes a favorable modification of an unwanted immune response in the subject desirous of such an effect.

Another aspect of the present invention is a method of treating unwanted immune response by administering a DSP composition to a subject in need thereof. In preferred embodiments, the subject is in need of such administration because of acute inflammation, rheumatoid arthritis, transplant rejection, asthma, inflammatory bowel disease, uveitis, restenosis, multiple sclerosis, psoriasis, wound healing, lupus erythematosus, pemphigus vulgaris, and any other autoimmune or inflammatory disorder that can be recognized by one of ordinary skill in the art. In other embodiments, the subject is in need of such administration because of Host versus Graft Disease (HVGD) or Graft versus Host Disease (GVHD), in the case of organ transplantation.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-D is a schematic depicting methodologies for designing synthetic peptide-based therapeutics. Panel A: how a peptide library is used for epitope discovery; Panel B: conceptual steps for generating Altered Peptide Ligand-based therapeutic; Panel C: a schematic of a dendrimer for multi-valent peptide presentation; Panel D: random sequence polymer generation.

FIG. 2 is a schematic for conceptual steps for generating Directed Sequence Polymers.

FIG. 3 shows the steps for preparing Directed Sequence Polymers.

FIG. 4 shows the preferred defined substitutive rules for directed expansion of epitope permeability.

FIG. 5 shows a generic rule structure and ranges of substitutions of DSP synthesis.

FIG. 6 shows an example of the application of the DSP Synthesis Rules using a mock-source peptide. RGDS and AKAVAAWTLKAAA peptides disclosed as SEQ ID NO: 239 and 236, respectively.

FIG. 7A-B shows an example of the application of the DSP Synthesis Rules using myelin basic protein (a.a. residues 83-99) as a source peptide.

FIG. 8A-C shows examples of the application of the DSP Synthesis Rules using an HLA-derived peptide and an HLA mimic-derived peptide as source peptides.

FIGS. 9A-9B shows an example of the application of the DSP Synthesis Rules using a GAD65-derived epitope peptide as a source peptide and applying an emprirically determined substitution rule. FIG. 9A disclosed SEQ ID NOS 47, 240, 82, 83 and 91, respectively, in order of appearance.

DETAILED DESCRIPTION OF THE INVENTION

It has previously been shown that mixtures of related peptides may be therapeutically more effective than a single peptide. Lustgarten et al., J. Immunol. 2006, 176: 1796-1805; Quandt et al., Molec. Immunol. 2003, 40: 1075-1087. The effectiveness of a peptide mixture as opposed to a single peptide is the likelihood of interaction with the broadening of the offending epitopes via the process of epitope spreading. (Immunol. Rev. 1998, 164:241) Therefore, to increase and maintain the effectiveness, these previous treatment modalities have been modified. For example, a therapeutic composition based on an APL may include multiple peptides created by the APL method in combination with the original peptide, or other APLs. Fairchild et al., Curr. Topics Peptide & Protein Res. 6, 2004. Each APL would have a defined sequence, but the therapeutic composition may be a mixture of APLs with more than one sequence. A reverse example involving conceptually similar altered peptide ligands involves an inventor's attempt to reduce the amount of variation created by pathogens to avoid immune recognition (viral alteration of immunogenic eptitopes over time, eg the creation of altered peptide ligands), by using the very changes created by the pathogen in an epitope sequence to create a limited diversity pool of peptides potentially useful in vaccinations (U.S. Pat. No. 7,118,874).

There have also been approaches to improving RSP, most notably upon COP-1. One can be seen in the work originated by Strominger et al. (WO/2003/029276) and developed further by Rasmussen et al. (US 2006/0194725) using RSP consisting of the amino acids Y, F, A, and K. Other than the change in amino acid content, the differences between the composition reside in the length (YFAK (SEQ ID NO: 215) is shorter than COP-1), and alanine content (YFAK (SEQ ID NO: 215) is suggested to have between 60-80% alanine, compared to _% of COP-1), which show as differences in the animal model data (YFAK (SEQ ID NO: 215) has better efficacy in EAE, the animal model of multiple sclerosis). Regarding the alanine content, Maurer (Pinchuck and Maurer, J. Exp Med 122(4), 673-9, 1965) described how an EAK polymer with higher alanine content (10-60 mole percent) produced “better antigens”, and Rasumussen et al. demonstrated that a YFAK (SEQ ID NO: 215) input ratio of 1:1:1:1 was not effective in eliciting a recall response as compared to a YFAK (SEQ ID NO: 215) preparation with an input ratio of 1:1:10:6.

Another attempt at improving upon COP-1 is described in WO/2005/032482 (the '482 publication). One interpretation of the '482 publication is that it is an attempt to make a more specific COP-1 by limiting the amount of diversity via the generation of ‘therapeutic ordered peptides’ for the treatment of multiple sclerosis. The '482 publication builds degenerate peptide sequences based not on actual peptide sequences, but on motifs. A preferred motif is [EYYK] (SEQ ID NO: 216), which is quite similar to the amino acid composition of COP-1 (YEAK) (SEQ ID NO: 217). The rationale for this motif teaches that the relative value placed on the inclusion of alanine as seen in the Maurer publication and Rasmussen et al. application discussed above is of a lesser importance The motifs are used as is, or can be altered by amino acid substitutions (defined on page 10-11 of the '482 publication). Much of the invention hinges on the presence of a D-amino acid at the amino terminal of the motif.

Yet another attempt at improving upon COP-1 is disclosed in WO/2005/074579 (the '579 publication). The application describes complex peptide mixtures containing A, E, K and Y of a length from 8-100 residues long. The disclosure contains preferred embodiments where the mixture also comprises AEKY (SEQ ID NO: 218), FLMY (SEQ ID NO: 219), IMQV (SEQ ID NO: 220), KRILV (SEQ ID NO: 221), FILMV (SEQ ID NO: 222), FWEF (SEQ ID NO: 223), EK, AEK, AKY, ANY, AINV (SEQ ID NO: 224), ASV, YEFW (SEQ ID NO: 225), Y, EFIVWY (SEQ ID NO: 226), EFKQ (SEQ ID NO: 227), AEKQ (SEQ ID NO: 228), AKQY (SEQ ID NO: 229), ANQY (SEQ ID NO: 230), AGNSY (SEQ ID NO: 231), AGINSV (SEQ ID NO: 232), AIQSV (SEQ ID NO: 233), IKRSVY (SEQ ID NO: 234), KHRV (SEQ ID NO: 235), HKR, PI, A, E, K, AE, AK, AY, EY, KY, AEY, EKY. The disclosure also contains diversity constraining mechanisms of defining amino acids at certain positions rather than being chosen by the random nature of the synthesis rules. The disclosure provides for a ratio of amino acids one to another for the AEKY (SEQ ID NO: 218) mixture as being similar to COP-1 at 1:1:6:3 YEAK (SEQ ID NO: 217).

The drawback of the these approaches is the undefined nature of what is effective in each motif, and quite possibly a large proportion of the peptides in the mixture may be inactive, lowering the concentration of the active components, or worse, adversely stimulating the immune system. Additionally, these compounds are difficult to manufacture and to obtain consistency from lot to lot.

Still another attempt at improving upon COP-1 can be seen in Strominger's efforts to design distinct, single 15mer peptide sequences who's amino acid composition resembles that of COP-1 and COP-1 related random sequence polymers. These single sequence fixed peptides were designed to increase an ability to compete for HLA-DR2 binding with the native myelin basic protein (MBP) peptide 85-99 (Stem et al., roc. Nat. Acad. Sci. USA, 102:1620-25). The drawback of this technology lies in the very nature of the attempt to determine discrete substitutes for the randomness that COP-1 encompasses.

The instant invention draws out the most useful properties of the previous treatment modalities yet removes the limitations of each. The instant invention utilizes: (1) the specific immunologic relevance of a defined epitope peptide, (2) the modulatory properties of an APL, (3) the multivalency of MAPs, (4) and the alanine content from RSP to generate a directed expansion via alteration and degeneration of epitope permeability that forms a complex yet directed peptide library useful for delivery as a therapeutic. The approach is schematically represented in FIG. 2.

The instant invention relates to a “Directed Sequence Polymer” (DSP). A DSP is a peptide having a sequence derived from a base peptide sequence, which may be but not limited to a native epitope associated with an unwanted immune response. A DSP has one or more amino acid residue that differs from that of the base peptide sequence, the substitution of which is determined by a defined rule. A DSP composition comprising multiple DSPs is synthesized by applying a set of synthesis rules that define the amino acid variations and the ratio of occurrence of introduction of such amino acid residues at any given position of the sequence to the base peptide sequence. Thus, a DSP is not synthesized as a single peptide, but is always synthesized as part of a composition comprising multiple related DSPs, the overall mixture of which is reproducible and consistent with the rules of synthesis that were applied. The schematic for the steps for creating a DSP composition, starting from the choice of a base peptide, is shown in FIG. 3.

I. Base Peptide Sequences

To create a meaningful DSP composition, one first needs to define the base peptide sequence to derive the DSPs from. The base peptide sequences can be derived in many ways. A peptide sequence useful for this purpose is a peptide sequence related to immune response in a mammal. These peptide sequences are, for example, partial sequences of certain heat shock proteins as an epitope, HLA derived peptide ligand sequences, organ-derived peptide sequences, and empirically derived peptide sequences, such as through screening of library created by a combinatory chemistry.

Heat Shock Protein-Derived Base Peptide Sequences.

A source of epitope sequence may be derived from heat shock proteins of any source or with the pathogen-derived mimic of a sequence within a mammalian heat shock protein (hsp). Mammalian heat shock proteins such as HSP-60 (Swiss-Prot primary accession number P10809), HSP-70 (Swiss-Prot primary accession number P08107), HSP-90 alpha (Swiss-Prot accession number P07900), HSP-90 beta (Swiss-Prot accession number P08238), or any protein having 75% homology to each are examples. Bacterial homologues of mammalian heat shock proteins include mycobacterial hsp65 (belonging to the hsp60 family)

Heat shock proteins as cellular chaperones that are known to be upregulated in response to stress signals have a high degree of potential pathophysiological disease mechanism involvement. Hsp, the peptides that derive from them, and their cross-species mimics have been implicated in central nervous system disease such as schizophrenia and multiple sclerosis (Schwarz et al., Am. J. Psychiatry, 1999, 156:1103-4; Battistine et al., Mol. Medicine, 1995, 1:554-62), atherosclerosis (Benagiano, et al., J. Immunol., 2005, 174:6509-17), rheumatoid arthritis (Anderton et al., J. Exp. Med., 1995, 181:943-52; van Roon et al., J. Clin. Invest., 1997, 100:459-63; Quintana et al., J. Immunol., 2003, 171:3533-41), systemic lupus erythematosus (Minota et al., J. Exp. Med., 1988, 168:1475-80), and diabetes (Raz et al., Lancet 358:1749-53).

HLA Derived Base Peptide Sequences

Immunologically relevant in a transplantation setting, HLA represent a large percentage of proteins to which recipient antibodies are directed. The gene products of HLA are seen to function as transplantation antigens. For example, studies analyzing the occurrence of acute graft versus host disease (GVHD) in relation to mismatched HLA alleles implicate the roles of HLA-DRB1 and HLA-DQB1 disparity between the donor and the recipient of a graft. Petersdorf et al., Proc. Nat. Acad. Sci. USA, 1996, 93: 15358-15363. Conversely, multiple examples of MHC-derived peptides have been reported as useful for immunotherapy. A study indicates that a large percentage of peptides bound to MHC on resting antigen presenting cells are MHC derived, leading to postulation that, other than functioning as stabilizers for the MHC heterodimers, these peptides may have roles in immunomodulation by competing with antigenic peptides, thereby increasing the threshold for antigenic stimulation. Murphy et al., J. Am. Soc. Nephrol., 2003, 14:1053-1065. Peptides derived from Class II MHC are indeed reported to act as T-cell regulatory factors. (LeGuern, Trends Immunol., 2003, 24:633-638). Further, synthetic peptides from a conserved region of class II MHC was able to mediate APC apoptosis and T cell hyporesponsiveness. Murphy, ibid. Elsewhere, a peptide derived from the predicted alpha helical domain of class II bound to I-Ak and inhibited antigen-dependent T-cell activation. Williams et al., Immunol. Res., 1992, 11:11-23. Peptides derived from Class I MHC are reported to exert effects on the immune system through various mechanisms, such as anergy, deletion, immune deviation, cell cycle prevention, disruption of antigen presentation, and inhibition of T cell activation. Murphy and Krensky, J. Am. Soc. Nephrol., 1999, 10:1346-1355.

Therefore, attenuating the immunological response to MHC is expected to reduce the severity and occurrence of GVHD. The above examples in the art showed the immunomodulatory effects using peptides having various contiguous amino acid sequences of HLA molecules. DSP based on the amino acid composition of HLA are expected to overcome such shortcomings and function as broadly relevant immunomodulators.

In an embodiment of the present invention, one or more epitopes comprising a mature HLA molecule are incorporated into the DSP. In another embodiment, one or more epitopes comprising the beta sheet of HLA are incorporated into the DSP. Synthetic peptides derived from the beta sheet of HLA-B7 have been shown to be immunodominant T-cell epitopes regulating alloresponses in GVHD. Freese and Zavazava (2002) Blood 99:3286-3292. These HLA-B7 derived allopeptides interfered with T cell mediated cytotoxicity targeted to HLA-B7 in vitro, and HLA-A2 derived allopeptides interfered with the cytotoxicity targeted to HLA-A2 in vitro, indicating allospecificity of these peptides.

Examples of amino acid compositions of HLA are provided herein. Known amino acid sequences of HLA proteins were obtained from GenBank and Swiss-Prot/trEMBL and were analyzed by using the ProtScale functions of ExPASy found at http://ca.expasy.org/cgi-bin/protscale.pl. Exemplary HLA sequences are GenBank Accession No. AAA36281, AAC02715, P01903 (alpha chain precursor), AAA17992, AAA59622 (heavy chain precursor), and AAA76608.

Organ Derived Base Peptide Sequences

A further category of derivation epitopes that may be useful for inducing tolerance are antigens derived from an organ to be transplanted itself. “Organ derived epitopes,” as defined herein, are: peptide epitopes comprising organ-specific proteins. These proteins are potentially important as antigens in a context of organ transplant. For example, it has been shown that donor allopeptides are continuously shed from grafts, resulting in indirect recognition of such donor allopeptides by the recipient T cells. This results in chronic organ transplant rejection and prevents sustained chimerism. For example, in cardiac allografts, chronic rejection is manifested as a diffuse and accelerated form of atherosclerosis, termed cardiac allograft vasculopathy. Lee et al. Proc. Nat. Acad. Sci. USA, 2001, 98: 3276-3281. Perhaps invoking the similar mechanism as that used by the MHC derived peptides, peptides derived from the transplanted organ may induce sustained chimerism by preventing the stimulation of immune response by the transplantation. The suppression of immunologic reaction to such allopeptide may contribute to preventing chronic rejection and aid to achieve sustained chimerism.

Hence, in another embodiment of the present invention, one or more epitopes comprising the organ-derived proteins of the organ subject to transplantation.

Other relevant organ-derived DSP may include the epitopes of proteins considered to be organ-specific. A DSP suitable for alleviating the immune reaction to transplantation of an organ and promoting sustained chimerism is designed based on the epitopes of organ-specific proteins for the organ being transplanted.

Liver: Organ specific antigens for liver includes bile salt export pump (GenBank accession number O95342), which is considered to be predominantly expressed on liver cells.

Heart: An example of a protein found specifically in heart is Atrial natriuteric peptide-converting enzyme (pro-ANP-converting enzyme) (Corin) (Heart specific serine proteinase ATC2) (Swiss-Prot Accession No. Q9Y5Q5).

Pancreas: An example of an organ-specific protein for human pancreas is carboxypeptidase B1 (GenBank Accession No. 32880163).

Kidney: An example of an organ-specific protein for kidney is chloride channel ClC-6c (GenBank Accession No. 1770380).

Spleen: An example of spleen specific protein is Spleen tyrosine kinase (SYK) (Swiss-Prot Accession No. P43405).

Lung: An example of lung specific protein is Plunc (Palate lung and nasal epithelium clone protein) (Lung specific X protein)(GenBank Accession No. 9801236).

Empirically Derived Base Peptide Sequences

As described in the above sections, peptide sequences with some significance to a disease state or an adverse reaction may be identified through experimental investigation of a relevant epitope. These sequences may include non-naturally occurring peptide sequences that proved to be useful in treating a disease or a condition, an example found in the international patent application publication WO 2006/031727, U.S. Pat. No. 6,930,168 and the related scientific publication Stem et al., Proc. Nat. Acad. Sci. USA, 2005, 102:1620-25.

Further, epitopes are empirically determined by identifying candidate sequences by positional scanning of synthetic combinatorial peptide libraries (see, for example, D. Wilson et al., above; R. Houghten et al., above; Hernandez et al., Eur J. Immunol., 2004, 34:2331-41), or by making overlapping peptide sequences of the entire protein of interest, and testing those peptides for immune reactivity (using, for example, any readout assay useful for such purposes, described in Current Protocols in Immunology Edited by John E Coligan, Ada M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strober NIH, John Wiley & Sons) in an in vitro or in vivo assay system appropriate for the disease and species the epitope is sought for. For example, for the design of a multiple sclerosis drug, an example of an appropriate system uses cells that derive from human subjects with MS.

After identifying a candidate epitope, a probable set of additional related epitopes are generated using modeling and prediction algorithms described in readily available references, for example WO 2000/042559, align and analyze the predicted binding of these probable epitopes using available prediction methods described in, for example, WO 2005/103679, WO 2002/073193 and WO 99/45954. Selecting from the peptides having the highest predicted activity/binding, take 40% of the predicted sequences and acquire the percentage of any given amino acid at each position. Use those percentages to create the rules for amino acid incorporation into a DSP synthesis.

Other Sources of Base Peptide Sequences

In addition to methodology and results described in the above sections, epitope sequences may be used as base peptide sequences, that are identified and included in the Immune Epitope Database, (available at http://www.immuneepitope.org/home.do, led by Alex Sette funded by the National Institute of Allergy and Infectious Diseases of the National Institute of Health, USA) or any sequences identified by processes performed and disclosed by commercial entities such as Mixtures Sciences of San Diego, or by Algonomics of Ghent Belgium.

Examples of epitopes identified as part of a naturally occurring, full length protein or synthetic peptides that were identified to have similar activities as such epitopes are shown in the table below.

TABLE I Examples of epitopes Source/ Representative Original SEQ ID Disease Peptide Sequence Protein Residue Number ref NO: Myasthenia KSYCEIIVTHFPFDEQNCSMK AChR a125-163, a256-269 35 1 gravis LGTWTYDGSVVATNPESD MKSDQESNNAAAEWKYVAM AChR a386-411, h 35 2 VMDHILL Rheumatoid FKGEQGPK Type II 263-270 38 3 Arthritis Collagen PKGQTGEBGIAGFKGEQGPK Type II 251-270 38 4 Collagen GEBGIAGFKGEQGPKGEBGP Type II 256-276 38 5 A Collagen Multiple EVGELSRGKLYSLGNGRWM CNPase 343-373 5 6 sclerosis LTLAKNMEVRAI GNGRWMLTLAKNMEVRAIFT CNPase 356-388 5 7 GYYGKGKPVPTQG ASQKRPSQRH MBP  1-10 8 LSRFSWGAEGQRPGFGYGG MBP 111-129 5 9 ASDYKSAHKGFKGVD MBP 131-145 10 ASDYKSAHKGLKGVDAQGTL MBP 131-155 5 11 SKIFK KYLATASTMDHARHGFLPRH MBP 13-32 5 12 KGFKGVDAQGTLSKI MBP 139-153 49 13 AQGTLSKIFKLGGRDSRSGS MBP 146-170 5 14 P-MARR GTLSKIFKLGGRDSR MBP 148-162 49 15 SHGRTQDENPWHFFK MBP 76-91 49 16 YGRTQDENPVVHFFKNIVTP MBP  80-103 49 17 RTPPP ENPVVHFFKNIVTPRTP MBP 83-99 5 18 DENPVVHFFKNIVTPRTPP MBP  84-102 49 19 ENPVVHFFKNIVTPR MBP 85-99 49 20 VVHFFKNIVTPRTPPPSQGK MBP  86-105 49 21 EKAKYEAYKAAAAAA Empirical 1 205 FSIHCCPPFTFNNSKKEIV MOBP 21-39 5 22 FLNSKKEIVDRKYSICKSG MOBP 31-49 5 23 CQFRVIGPRHPIRALVGDEV MOG  1-20 5 24 PIRALVGDEVELPCRISPGK MOG 11-30 5 25 ELPCRISPGKNATGMEVGWY MOG 21-40 5 26 MEVGWYRPPFSRVVHLYRN MOG 35-55 5 27 GK HSLGKWLGHPDKF PLP 139-151 28 HCLGKWLGHPDKFVGI PLP 139-154 5 29 NTWTTCQSIAFPSKTSASIG PLP 178-197 5 30 SKTSASIGSLCADARMYGVL PLP 190-209 5 31 GFYTTGAVRQIFGDYKTT PLP  89-106 5 32 Penphigus REWVKFAKPCRE Dsg3 49-60 8 33 vulgaris QATQKITYRISGVGIDQ Dsg3 78-94 45 34 PFGIFVVDKNTGDINIT Dsg3  96-112 45 35 HLNSKIAFKIVSQEPAG Dsg3 189-205 45 36 GTPMFLLSRNTGEVRTL Dsg3 205-221 45 37 QCECNIKVKDVNDNFPM Dsg3 250-266 45 38 SVKLSIAVKNKAEFHQS Dsg3 342-358 45 39 NVREGIAFRPASKTFTV Dsg3 376-392 45 40 RDSTFIVNKTITAEVLA Dsg3 483-499 45 41 SARTLNNRYTGPYTF Dsg3 512-526 48 42 QSGTMRTRHSTGGTN Dsg3 762-786 48 43 Insulin AALGIGTDSVILIKCDERGK GAD65 10 44 Dependent Diabetes AFTSEHSHFSLKKGAAALGI GAD65 10 45 ATHQDIDFLIEEIERLGQDL GAD65 10 46 AVRPLWVRME GAD65 46 47 AYVRPLWVRME GAD65 46 48 CGRHVDVFKLWLMWRAKGT GAD65 10 49 TG DERGKMIPSDLERRILEAKQ GAD65 10 50 DICKKYKIWMHVDAAWGGGLL GAD65 10 51 MS DMVGLAADWLTSTANTNMFT GAD65 10 52 EEILMHCQTTLKYAIKTGHP GAD65 10 53 ELLQEYNWELADQPQNLEEIL GAD65 10 54 M ERANSVTWNPHKMMGVPLQ GAD65 10 55 C EYGTTMVSYQPLGDKVNFFR GAD65 10 56 EYLYNIIKNREGYEMVFDGK GAD65 10 57 EYVTLKKMREIIGWPGGSGD GAD65 10 58 GGSGDGIFSPGGAISNMYAM GAD65 10 59 GLLMSRKHKWKLSGVERANS GAD65 10 60 GSGDSENPGTARAWCQVAQK GAD65 10 61 FTG HATDLLPACDGERPTLAFLQ GAD65 10 62 IPPSLRTLEDNEERMSRLSK GAD65 10 63 KGTTGFEAHVDKCLELAEYL GAD65 10 64 YN KHYDLSYDTGDKALQCGRHV GAD65 10 65 KPCSCSKVDVNYAFLHATDL GAD65 10 66 KTGHPRYFNQLSTGLDMVGL GAD65 10 67 KVAPVIKARMME GAD65 46 68 KVAPVWVARMME GAD65 46 69 KVAPVWVRME GAD65 46 70 LAFLQDVMNILLQYVVKSFDR GAD65 10 71 S LEAKQKGFVPFLVSATAGTT GAD65 10 72 LLYGDAEKPAESGGSQPPRA GAD65 10 73 LSKVAPVIKARMMEYG GAD65 526-541 46 74 MASPGSGFWSFGSEDGSGDS GAD65 10 75 NMYAMMIARFKMFPEVKEKG GAD65 10 76 PEVKEKGMAALPRLIAFTSE GAD65 10 77 QHRPLWVRME GAD65 46 78 QKFTGGIGIGNKLCALLYGD GAD65 10 79 QNCNQMHASYLFQQDKHYD GAD65 10 80 L QPPRAAARKAACACDQKPC GAD65 10 81 SC RTRPLWVRME GAD65 46 82 RVLPLWVRME GAD65 46 83 SFDRSTKVIDFHYPNELLQE GAD65 10 84 SRLSKVAPVIKARMMEYGTT GAD65 524-543 46 85 TAGTTVYGAFDPLLAVADICK K GAD65 10 86 TNMFTYEIAPVFVLLEYVTL GAD65 10 87 VFDGKPQHTMVCKWYIPPSL GAD65 10 88 VNFFRMVISMPAATHQDIDF GAD65 10 89 VPLQCSALLVREEGLMQNCNQ GAD65 10 90 YTLPLWVRME GAD65 46 91 systemic lupus QCSDISTKQMFKAVSEVCRI human 101-125 28 92 erythematosus PTHL Ro60 ETEKLLKYLEAVEKVKRTRDE human 221-245 28 93 LEVI Ro60 KARIHPFHILIALETYKTGH hRo60 316-335 15 94 FKTVEPTGKRFLLAVDVSAS human 361-385 28 95 MNQRV Ro60 MNQRVLGSILNASTVAAAMCI human 381-405 28 96 KALDA Ro60 PCPVTTDMTLQQVLMAMSQI human 421-445 28 97 PAGGT Ro60 PAGGTDCSLPMIWAQKTNTP hRo60 441-465 15 98 ADVFI KTNTPADVFIVFTDNETFAG human 456-475 28 99 Ro60 MAALEAKICHQIEYYF La/SSB 10-25 20 100 DEYKNDVKNRSVYIKGFPTD La/SSB 102-127 20 101 ATLDDI RSVYIKGFPTDATLDD La/SSB 111-126 20 102 TLDDIKEWLEDKGQVL La/SSB 123-138 20 103 WLEDKGQVLNIQMRRT La/SSB 130-145 20 104 KGQVLNIQMRRTLHKAFKGSI La/SSB 134-169 20 105 FVVFDSIESAKKFVE MRRTLHKAFKGSIFVV La/SSB 142-157 20 106 SIFVVFDSIESAKKFV La/SSB 153-168 20 107 VVFDSIESAKKFVETP La/SSB 156-171 20 108 SIESAKKFVETPGQKY La/SSB 160-175 20 109 TDLLILFKDDYFAKKNE La/SSB 178-194 20 110 ILFKDDYFAKKNEERK La/SSB 182-197 20 111 CHQIEYYFGDFNLPRDKFLK La/SSB 18-37 20 112 EEDAEMKSLEEKIGCL La/SSB 218-233 20 113 LEEKIGCLLKFSGDLD La/SSB 226-241 20 114 YYFGDFNLPRDKFLKE La/SSB 23-38 20 115 SNHGEIKWIDFVRGAK La/SSB 254-269 20 116 GEIKWIDFVRGAKEGI La/SSB 257-272 20 117 ALKGKAKDANNGLNQLR La/SSB 282-297 20 118 FNLPRDKFLKEQIKLD La/SSB 28-43 20 119 AKDANNGNLQLRNKEV La/SSB 286-301 20 120 LQLRNKEVTWELVEGE La/SSB 294-309 20 121 NKEVTWELVEGEVEKE La/SSB 298-313 20 122 EGEVEKEALKKIIEDQ La/SSB 307-322 20 123 EKEALKKIIEDQQESL La/SSB 311-326 20 124 RDKFLKEQIKLDEGWV La/SSB 32-47 20 125 GKGKGNKAAQPGSGKG La/SSB 338-353 20 126 GSKGKGKVQFQGKKTK La/SSB 349-363 20 127 FQGKKTKFASDDEHDE La/SSB 357-372 20 128 DENGATGPVKRAREET La/SSB 377-389 20 129 EETDKEEPASKQQKTE La/SSB 387-402 20 130 GWVPLEIMIKFNRLNRLTTDF La/SSB 45-67 20 131 NV PLEIMIKFNRLNRLTT La/SSB 48-63 20 132 IMIKFNRLNRLTTDFN La/SSB 51-66 20 133 KFNRLNRLTTDFNVIV La/SSB 54-69 20 134 DFNVIVEALSKSKAEL La/SSB 64-79 20 135 LSKSKAELMEISEDKT La/SSB 72-87 20 136 SKAELMEISEDKTKIR La/SSB 75-90 20 137 RRSPSKPLPEVTDEY La/SSB  89-104 20 138 PSKPLPEVTDEYKNDV La/SSB  93-108 20 139 KFGADARALMLQGVDLLADA human 31-50 34 140 HSP60 autoimmunity LKVGLQVVAVKAPGF human 291-305 12 141 in general HSP60 GGAVFGEEGLTLNLE human 321-335 12 142 HSP60 TLNLEDVQPHDLGKV human 331-345 12 143 HSP60 VGAATEIEMKEKKDR human 381-395 12 144 HSP60 VGGTSDVEVNEKKDR human 406-420 12 145 HSP60 IVLGGGCALLRCIPA human 436-450 12 146 HSP60 VLGGGVALLRVIPALDSLTPA human 437-460 36 147 NED HSP60 GCALLRCIPALDSLT human 441-455 12 148 HSP60 RCIPALDSLTPANED human 446-460 12 149 HSP60 EIIKRTLKIPAMTIA human 446-480 12 150 HSP60 VEKIMQSSSEVGYDA human 491-505 12 151 HSP60 MAGDFVNMVEKGIID human 506-520 12 152 HSP60 VNMVEKGIIDPTKVV human 511-525 12 153 HSP60 VAVTMGPKGRTVIIE human 51-65 12 154 HSP60 KGIIDPTKVVRTALL human 516-530 12 155 HSP60 PTKWRTALLDAAGV human 521-535 12 156 HSP60 ASLLTTAEWVTEIP human 536-550 12 157 HSP60 GETRKVKAH HLA-A2 62-70 18 158 RKVKAHSQTHRVDLG HLA-A2 65-79 18 159 RVDLGTLRGYYNQSE HLA-A2 75-89 18 160 DGRLLRGHDQYAYDG HLA-B7 106-120 18 161 GPEYWDRNTQIYKA HLA-B7 56-69 18 162 WDRNTQIYKAQAQTDR HLA-B7 60-75 18 163 RNTQIYKAQ HLA-B7 62-70 18 164 RESLRNLRGYYNQSE HLA-B7 75-89 18 165 GSHTLQSMYGCDVGP HLA-B7  91-105 18 166 LNEDLRSWTAAD HLA-B7 150-161 19 167 LNEDLRSWTAABTAA HLA-B7 150-164 19 168 DKGQVLNIQ HLA-DQ2 133-142 20 169 LEDKGQVLNIQMRR HLA-DQ2 131-144 20 170 AFKGSIFVVFDSIE HLA-DQ2 149-162 20 171 ESAKKFVET HLA-DQ2 162-170 20 172 IESAKKFVETPGQK HLA-DQ2 161-174 20 173 AKDANNGNLQLR HLA-DQ2 286-297 20 174 EALKKIIED HLA-DQ2 311-324 20 175 EQIKLDEGW HLA-DQ2 36-47 20 176 LKEQIKLDEGWV HLA-DQ2 36-47 20 177 AELMEISED HLA-DQ2 75-87 20 178 SKAELMEISEDKT HLA-DQ2 75-87 20 179 KGSIFWFD HLA- 149-162 20 180 DQ2, DQ7 AKDANNGNLQLRNK HLA 286-299 20 181 DQ2, DQ7 DANNGNLQL HLA- 288-299 20 182 DQ2, DQ7 IVEALSKSKAEL HLA 66-80 20 183 DQ2, DQ7 AFKGSIFVVFDSI HLA-DQ7 149-161 20 184 GSIFVVFDSIESAK HLA-DQ7 152-165 20 185 IFWFDSIESAKKF HLA-DQ7 154-167 20 186 WFDSIESA HLA-DQ7 154-167 20 187 ELMEISEDKTKIR HLA-DQ7 78-90 20 188 EALYLVCGE HLA-DQ8 35-47 20 189 II. Rules of Synthesis for Directed Sequence Polymers

Steps in the creation of a DSP sequentially encompass the following:

(a) Identify a protein having known or believed association with a pathology.

(b) Select from within the protein a peptide or peptides, each having a fixed sequence, that are associated with the pathology and immunologically relevant. If no peptides have been described, then peptides useful in the treatment of the pathology of interest are created. One exemplary method is to create a library of peptides that collectively span the entire length of the protein of interest. This may be done by, for example, partial endopeptidase digestion or by peptide synthesis. The library is screened for immunologically relevant peptides using appropriate detection methods such as binding affinity determination using antibodies detected in the sera of patients with the target pathology. The peptides may be further examined for immunogenicity useful for the treatment of the pathology in an in vitro or in vivo experimental system.

(c) the amino acid substitutions are decided based on either of two sets of rules, defined or empirical and are set forth below;

(d) Solid phase synthesis of DSP according to the rules is performed, and pharmaceutically acceptable formulation the DSP is delivered as a therapeutic.

The rules of synthesis for a composition comprising DSPs are outlined below. Briefly, a DSP may be envisioned as a polypeptide having a defined length that is either the same length as or multiples of the length of the base peptide sequence. For each residue position of the base peptide sequence, one or more substitute residue is defined. The rule of synthesis defines the ratio among the original base peptide residue for that position, the first substitute residue, the second substitute residue, the third substitute residue, and an alanine, to occupy any given residue position.

The substitute residues are defined according either: (1) to a rational comparison and finding of similarities of relevant characteristics of the original residue with those of the substitute residue or (2) to a comparison of reported experimental results on the relative activities of actual peptides having slight variations from the base sequence. The substitute residues defined in either of these two approaches are termed “conserved substitution” herein.

An example of a rational comparison and findings of similarity is the methods described by Kosiol et al., J. Theoretical Biol., 2004, 228:97-106. Amino acids are grouped together in a matrix, referred therein as PAM replacement matrix. FIG. 4 is a table showing the amino acid similarity and grouping, according to Kosiol, based on the characteristics of the residues such as size, charge, hydrophobicity, etc., as shown in Table X of the reference. In FIG. 4, amino acids grouped together are considered interchangeable, with high likelihood of retaining characteristics common among the group,

A comparison of experimental results showing the relative activities of peptides having slight variations from the base sequence can also be used as a basis for the rule for substitution. The sequences of the peptides responsible for observed changes are aligned and the type and percent presence of the new amino acid are noted. If there is more than one amino acid substitution at any given position of the peptide, the frequency of occurrence of an amino acid and the magnitude of activity change compared to the original sequence are taken into account to determine the order of prevalent substitution. Examples of the overall process leading up to the rule generation for DSP synthesis can be found using libraries (Molec. Immunol. 40:1047-1055; Molec. Immunol. 40:1063-74; J Autoimmunity 20:199-201; and J Immunol 163:6424-34), by making altered peptide ligands of overlapping peptides representing the entire protein of interest (Atkinson et al., J. Clin. Invest. 94:2125-29; Meini et al., J. Clin. Invest. 92:2633-43) or de novo (U.S. Pat. Nos. 7,058,515; 6,376,246; 6,368,861; 7,024,312; 6,376,246; 7,024,312; 6,961,664; 6,917,882). Briefly, a cellular material of interest is chosen as the assay system to rank the immunoreactivity of the peptides to be interrogated. Such an assay system can be either an in vitro or in vivo system, and can comprise adaptive or innate immune reactivity. Readouts for the assay system can be the up- or down-regulation of the status of the activation state of a protein, a change in the localization of a protein, the expression of the mRNA encoding for the protein, the relative concentration of a protein, changes in the generation of specific cell types, changes in cellular phenotype, changes in cellular activation, changes in cell number, changes in organ size or function, changes in animal behavior or phenotype. Once the assay or assays are performed the results are analyzed to determine the prevalence of any particular amino acid as a conserved substitution. If more than three residues in a given position within the peptide sequence are identified as generating a change in immunologic function, the top three residues first by frequency of representation in the interrogated peptides, and second by the magnitude of changes elicited. Once chosen, the relative amounts of the residues are defined. As depicted in FIG. 5, each cassette, “y”, has a set of amino acid ratios one to another that have a range of about 0-100 for the base (a), the primary change (b), the secondary change (c), and the tertiary change (d), whereas alanine (e) has a ratio of about 5-1000. The rules for the DSP synthesis continue with the combination of the cassettes in the order prescribed. The same block can be repeated either sequentially or separated by another block. On either side of the cassette sequence are N- and C-terminal modifiers. The number of cassettes is dictated by the requirements of the end length of the DSP which is required to be longer than 25 amino acids and shorter than 300 amino acids.

As described in FIG. 6, the instant invention envisions multiple epitopes to be defined as separate cassettes and synthesized sequentially. Cassette ratios within the same DSP may have different ratios of amino acids. Further, if there is less than three non-alanine amino acid substitutions, the percentage of the ‘missing’ substitution is added to the base sequence. Further, a cassette may be placed in any order with multiple appearances in the overall DSP synthesis. The N- and C-terminal Modifications reside prior to and after the entirety of the DSP cassettes respectively. As seen in FIG. 7A, a single base peptide sequence may have more than one ratio defined as a separate cassette in this example y1, y2, and y3. The individual cassettes can be placed in any order with multiple appearances in the overall DSP synthesis as seen in FIG. 7B. The synthesis rules seen in FIGS. 8A and 8B describe a DSP of the instant invention having portions of a single base peptide sequence with more than one ratio defined as a separate cassette.

FIG. 9 demonstrates how the instant invention envisions empirically derived ratios of amino acids at a particular position. The example uses data derived from a T cell activation assay using diabetogenic T cells derived from transgenic NOD.BCD2.5 mice (J. Immunol. 166:908-17; J Autoimmunity 20:199-201). The cells re interrogated with a combinatorial decamer library which resulted in a number of different peptides with inhibitory activity. The peptides with the highest activity were used to generate the amino acids at each position, as well as the ratio of different amino acids one to another.

A cassette may be repeated more than once. After a desired number of multiples of the cassette, if the desired length of the DSP is not yet reached, the DSP sequence is further defined by applying the same process, possibly using different ratio among the original, substitute, second substitute, and alanine residues.

N or C-terminal DSP modifiers may be added to the synthesis rules. The purpose of such modifiers include but are not limited to enhancing binding to specific proteins as in the case of RDG-based amino acid sequences (U.S. Pat. No. 5,773,412; 5,770,565) used as targeting moieties, or peptides that are known to bind to a wide array of HLA-DR species, such as AKAVAAWTLK AAA (SEQ ID NO: 236) (U.S. App. Pub. No. 2006/0018915) as a DR-targeting moiety. Such modifiers may include moieties which enhance complexation to delivery systems including sustained release delivery systems. Modifiers can be resorbable matrix constructs/synthesizable backbones such as PLGA. Modifiers can be protease resistant moieties such as D-amino acids.

Thus, for any given base peptide sequence, a set of synthesis rules is applied to yield a composition comprising reproducible, consistent mixture of DSPs.

III. Peptide Synthesis Methods

Any known solid phase synthesis appropriate for peptide synthesis may be used to synthesize a composition comprising DSPs, for example as originally described by Merrifield (J. Am. Chem. Soc., 1963, 85:2149) and any variation thereof. More specifically, the synthesis is done in multiple steps by the Solid Phase Peptide Synthesis (SPPS) approach using Fmoc protected amino acids. SPPS is based on sequential addition of protected amino acid derivatives, with side chain protection where appropriate, to a polymeric support (bead). The base-labile Fmoc group is used for N-protection. After removing the protecting group (via piperidine hydrolysis) the next amino acid mixture is added using a coupling reagent (TBTU). After the final amino acid is coupled, the N-terminus is acetylated.

The resulting peptides (attached to the polymeric support through its C-terminus) are cleaved with TFA to yield the crude peptide. During this cleavage step, all of the side chains protecting groups are also cleaved. After precipitation with diisopropyl ether, the solid is filtered and dried. The resulting peptides are analyzed and stored at 2-8° C.

Additionally, any peptide synthesis method that allows synthesis incorporating more than one amino acid species at a controlled ratio in any given position of the peptide sequence is suitable for use with this invention. Further, as described below, DSPs may be peptidomimetics or include unnatural or modified amino acid, necessitating the adaptation to allow addition of such chemical species to the polymers synthesized up to that point.

The synthesis may include unnatural amino acids, or amino acid analogs. In some embodiments, the DSPs are comprised of naturally occurring and synthetic derivatives, for example, selenocysteine. Amino acids further include amino acid analogs. An amino acid “analog” is a chemically related form of the amino acid having a different configuration, for example, an isomer, or a D-configuration rather than an L-configuration, or an organic molecule with the approximate size and shape of the amino acid, or an amino acid with modification to the atoms that are involved in the peptide bond, so as to be protease resistant when polymerized in a polypeptide.

The DSPs for use in the present invention can be composed of L- or D-amino acids or mixtures thereof. As is known by those of skill in the art, L-amino acids occur in most natural proteins. However, D-amino acids are commercially available and can be substituted for some or all of the amino acids used to make DSPs of the present invention. The present invention contemplates DSPs containing both D- and L-amino acids, as well as DSPs consisting essentially of either L- or D-amino acids.

In certain embodiments, the DSPs of the present invention include such linear DSPs that are further modified by substituting or appending different chemical moieties. In one embodiment, such modification is at a residue location and in an amount sufficient to inhibit proteolytic degradation of the DSPs in a subject. For example, the amino acid modification may be the presence in the sequence of at least one proline residue; the residue is present in at least one of carboxy- and amino termini; further, the proline can be present within four residues of at least one of the carboxy- and amino-termini. Further, the amino acid modification may be the presence of a D-amino acid.

In certain embodiments, the subject DSPs is a peptidomimetic. Peptidomimetics are compounds based on, or derived from, peptides and proteins. The DSP peptidomimetics of the present invention typically can be obtained by structural modification of one or more native amino acid residues, e.g., using one or more unnatural amino acids, conformational restraints, isosteric replacement, and the like. The subject peptidomimetics constitute the continuum of structural space between peptides and non-peptide synthetic structures.

Such peptidomimetics can have such attributes as being non-hydrolyzable (e.g., increased stability against proteases or other physiological conditions which degrade the corresponding peptide DSPS), increased specificity and/or potency. For illustrative purposes, peptide analogs of the present invention can be generated using, for example, benzodiazepines (e.g., see Freidinger et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p 123), C-7 mimics (Huffman et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p. 105), keto-methylene pseudopeptides (Ewenson et al. J. Med. Chem., 1986, 29:295; and Ewenson et al. in “Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium),” Pierce Chemical Co. Rockland, Ill., 1985), β-turn dipeptide cores (Nagai et al., Tetrahedron Lett., 1985 26:647; and Sato et al. J. Chem. Soc. Perkin Trans., 1986, 1:1231), β-aminoalcohols (Gordon et al. Biochem. Biophys. Res. Commun., 1985, 126:419; and Dann et al. Biochem. Biophys. Res. Commun., 1986, 134:71), diaminoketones (Natarajan et al. Biochem. Biophys. Res. Commun., 1984, 124:141), and methyleneamino-modified (Roark et al. in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p 134). Also, see generally, Session III: Analytic and synthetic methods, in “Peptides: Chemistry and Biology,” G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988.

The molecular weight of a DSP composition can be adjusted during polypeptide synthesis or after the DSPs have been synthesized. To adjust the molecular weight during polypeptide synthesis, the synthetic conditions or the amounts of amino acids are adjusted so that synthesis stops when the polypeptide reaches the approximate length which is desired. After synthesis, polypeptides with the desired molecular weight can be obtained by any available size selection procedure, such as chromatography of the polypeptides on a molecular weight sizing column or gel, and collection of the molecular weight ranges desired. The present polypeptides can also be partially hydrolyzed to remove high molecular weight species, for example, by acid or enzymatic hydrolysis, and then purified to remove the acid or enzymes.

In one embodiment, the DSPs with a desired molecular weight may be prepared by a process which includes reacting a protected polypeptide with hydrobromic acid to form a trifluoroacetyl-polypeptide having the desired molecular weight profile. The reaction is performed for a time and at a temperature which is predetermined by one or more test reactions. During the test reaction, the time and temperature are varied and the molecular weight range of a given batch of test polypeptides is determined. The test conditions which provide the optimal molecular weight range for that batch of polypeptides are used for the batch. Thus, a trifluoroacetyl-polypeptide having the desired molecular weight profile can be produced by a process which includes reacting the protected polypeptide with hydrobromic acid for a time and at a temperature predetermined by test reaction. The trifluoroacetyl-polypeptide with the desired molecular weight profile is then further treated with an aqueous piperidine solution to form a low toxicity polypeptide having the desired molecular weight.

In one preferred embodiment, a test sample of protected polypeptide from a given batch is reacted with hydrobromic acid for about 10-50 hours at a temperature of about 20-28° C. The best conditions for that batch are determined by running several test reactions. For example, in one embodiment, the protected polypeptide is reacted with hydrobromic acid for about 17 hours at a temperature of about 26° C.

IV. Pharmaceutical Composition

One aspect of the present invention is a pharmaceutical composition comprising a DSP composition. As described below in the method of treatment as an aspect of this invention, the DSP composition produced by the process of the invention is useful in treatment of unwanted immune response, such as autoimmune diseases and transplantation rejection in a subject.

The DSPs of the present invention may be administered to the subject as a composition which comprises a pharmaceutically effective amount of DSPs and an acceptable carrier and/or excipients. A pharmaceutically acceptable carrier includes any solvents, dispersion media, or coatings that are physiologically compatible. Preferably, the carrier is suitable for oral, rectal, transmucosal (including by inhalation), parenteral, intravenous, intramuscular, intraperitoneal, intradermal, transdermal, topical, or subcutaneous administration. One exemplary pharmaceutically acceptable carrier is physiological saline. Other pharmaceutically acceptable carriers and their formulations are well-known and generally described in, for example, Remington's Pharmaceutical Science (18^(th) Ed., ed. Gennaro, Mack Publishing Co., Easton, Pa., 1990). Various pharmaceutically acceptable excipients are well-known in the art and can be found in, for example, Handbook of Pharmaceutical Excipients (4^(th) ed., Ed. Rowe et al. Pharmaceutical Press, Washington, D.C.). The composition can be formulated as a solution, microemulsion, liposome, capsule, tablet, or other suitable forms. The active component which comprises the copolymer may be coated in a material to protect it from inactivation by the environment prior to reaching the target site of action. The pharmaceutical compositions of the present invention are preferably sterile and non-pyrogenic at the time of delivery, and are preferably stable under the conditions of manufacture and storage. When desirable, the composition further comprises components to enhance stability, permeability, and/or bioavailability, such as particulate forms protective coatings, protease inhibitors or permeation enhancers for various routes of administration, including parenteral, pulmonary, nasal and oral.

For oral administration, the pharmaceutical preparation may be in liquid form, for example, solutions, syrups or suspensions, or may be presented as a drug product for reconstitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pre-gelatinized maize starch, polyvinyl pyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulfate). The tablets may be coated by methods well-known in the art.

In one embodiment, the oral composition is enterically-coated. Use of enteric coatings is well known in the art. For example, Lehman (1971) teaches enteric coatings such as Eudragit S and Eudragit L. The Handbook of Pharmaceutical Excipients, 2^(nd) Ed., also teaches Eudragit S and Eudragit L applications. One Eudragit which may be used in the present invention is L30D55. Preparations for oral administration may be suitably formulated to give controlled release of the active compound.

The compositions may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

For administration by inhalation, the compositions for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin, for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The compositions may be formulated for administration by injection, e.g., by bolus injection or continuous infusion in a parenteral, intravenous, intraperitoneal, intramuscular, or subcutaneous manner. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for reconstitution with a suitable vehicle, e.g., sterile pyrogen free water, before use.

In a preferred embodiment, compositions comprising DSP compositions are formulated in accordance with routine procedures as pharmaceutical compositions adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline, with the intervals between administrations being greater than 24 hours, 32 hours, or more preferably greater than 36 or 48 hours. Where the composition is administered by injection, an ampoule of sterile water or saline for injection can be provided so that the ingredients may be mixed prior to administration.

In other embodiments of the present invention, the pharmaceutical compositions are regulated-release or sustained release formulations. DSP compositions of the present invention may be admixed with biologically compatible polymers or matrices which control the release rate of the copolymers into the immediate environment. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). One embodiment of sustained release formulations is transdermal patches.

In some embodiments of the present invention, pharmaceutical compositions comprise DSPs formulated with oil and emulsifier to form water-in-oil microparticles and/or emulsions. The oil may be any non-toxic hydrophobic material liquid at ambient temperature to about body temperature, such as edible vegetable oils including safflower oil, soybean oil, corn oil, and canola oil; or mineral oil. Chemically defined oil substance such as lauryl glycol may also be used. The emulsifier useful for this embodiment includes Span 20 (sorbitan monolaurate) and phosphatidylcholine. In some embodiments, a DSP composition is prepared as an aqueous solution and is prepared into an water-in-oil emulsion dispersed in 95 to 65% oil such as mineral oil, and 5 to 35% emulsifier such as Span 20. In another embodiment of the invention, the emulsion is formed with alum rather than with oil and emulsifier. These emulsions and microparticles reduce the speed of uptake of DSPs, and achieve controlled delivery.

In another embodiment, the controlled and/or sustained delivery is achieved by implantable medical devices coated with sustained-release formulations, or implantable pharmaceutical formulation suitable for sustained-release of the active components.

In some embodiments of the invention, pharmaceutical compositions comprise a set of nucleic acid vectors encoding a DSP composition, which is expressed as polypeptides within a subject. The vectors may comprise transcription- and/or translation-controlling elements such that the timing and level of the DSPs composition produced may be regulated.

In some embodiments, the vectors also comprise one or more additional coding sequences, which encodes a therapeutically beneficial polypeptide or a second, different composition of DSPs that is not a member of the first DSP composition. In alternative embodiments, a pharmaceutical composition comprises one or more vectors, each encoding either: the DNA sequences for the DSPs of a first DSP composition, or the DNA sequences for the DSPs of a second DSPs composition or a therapeutically beneficial polypeptide, that is not a member of the first DSP composition. Such therapeutically beneficial polypeptide may be, for example, an immunomodulatory cytokine or a growth factor.

Some embodiments of the invention are pharmaceutical compositions for targeted delivery of the DSP composition of the invention. In such embodiments, a pharmaceutical composition comprises a DSP composition that is complexed with a targeting moiety. The targeting moiety allows localized delivery of the DSP composition to a desired location or microenvironment within the subject. A targeting moiety include, and may be selected from, the group comprising a chemical group or functionality such as biotin or simple sugars, a single or double stranded DNA sequence of various lengths, a single or double stranded RNA sequence of various lengths, a peptide of various lengths, an antibody including single chain antibodies, Fab′, or modified antibodies, a lipid, or a glycolipid. More than one of such moiety may be used at the same time in combination. For examples of targeting moieties, see U.S. Pat. No. 6,268,488; U.S. Appl. Pub. No. 2003/0190676; and see, for example, www.covx.com/tech_creating.html.

In one embodiment of the invention, the complex has characteristics of a prodrug, causing the DSP composition to exhibit no pharmaceutical activity of the present invention until the dissolution of the complex in the subject. In another embodiment, the complex does not affect the activity of the DSP composition.

Any methods generally known to one skilled in the art may be used to produce a complex of the instant invention and a targeting moiety. The target moiety may be complexed to the DSPs by a chemical bond, which may be covalent, ionic, hydrophobic, or van der Waals force, directly or through another chemical entity. Alternatively, the target moiety may be co-localized with the DSPs through common medium such as a biocompatible resin within which the DSP composition is included. The manner of forming a complex is chosen also based on the active state of the instant invention while existing in the combination and whether a permanent complex or a transitory complex is desired.

In some embodiments, the pharmaceutical compositions also include additional therapeutically active agents. Such additional ingredient can be at least an additional DSP composition that binds to a different target, an antibody which binds to an unwanted inflammatory molecule or cytokine such as interleukin-6, interleukin-8, granulocyte macrophage colony stimulating factor, and tumor necrosis factor-α; an enzyme inhibitor such as a protease inhibitor aprotinin or a cyclooxygenase inhibitor; an antibiotic such as amoxicillin, rifampicin, erythromycin; an antiviral agent such as acyclovir; a steroidal anti-inflammatory such as a glucocorticoid; a non-steroidal anti-inflammatory such as aspirin, ibuprofen, or acetaminophen; or a non-inflammatory cytokine such as interleukin-4 or interleukin-10. Other cytokines and growth factors such as interferon-β, tumor necrosis factors, antiangiogenic factors, erythropoietins, thrombopoietins, interleukins, maturation factors, chemotactic protein, and their variants and derivatives that retain similar physiological activities may also be used as an additional ingredient.

Further, a form of vitamin D that is or becomes biologically active within the body of the subject receiving such form of vitamin D may also be used as an additional ingredient. The two main forms of vitamin D are: vitamin D3 or cholecalciferol, which is formed in the skin after exposure to sunlight or ultraviolet light, and ergocalciferol or vitamin D2 which is obtained by irradiation of plants or plant materials or foods. The differences are situated in the side chain. Vitamin D3 may be obtained from natural sources such as fatty fish such as herring and mackerel. In the body, two other forms of vitamin D3 can be found. Vitamin D3 is hydroxylated in the liver into 25-hydroxyvitamin D3 (25(OH)D), and subsequently in the kidney into 1,25-dihydroxyvitamin D3 (1,25(OH)2D), which is the active metabolite that stimulates the calcium absorption from the gut (Feldman et al., 2005). When 1,25(OH)2D is sufficiently available, 24,25-dihydroxyvitamin D (24,25(OH)2D) is formed in the kidney, which is further catabolized.

Another class of therapeutically active agents useful as an additional agent is immune boosters which increases the production of common lymphoid precursors (CLPs) from the multilineage potential cells. An example of such agent is PBI-1402 developed by ProMetic in Quebec, Canada.

In some embodiments, the additional active therapeutically active agent is selected from the group consisting of anti-psoriasis creams, Sulfasalazine, glucocorticoids, propylthiouracil, methimazole, I¹³¹, insulin, IFN-β1a, IFN-β1b, glucocorticoids, ACTH, avonex, azathiopurine, cyclophosphamide, UV-B, PUVA, methotrexate, calcipitriol, cyclophosphamide, OKT3, FK-506, cyclosporin A, azathioprine, and mycophenolate mofetil.

Another class of therapeutic agents that are useful to combine with the DSP composition of the invention is anti-obesity drugs, for example Lipitor. Anti-obesity drugs include P-3 agonists, CB-1 antagonists, appetite suppressants, such as, for example, sibutramine (Meridia), and lipase inhibitors, such as, for example, or list at (Xenical). The subject copolymers may also be used in methods of the invention in combination with drugs commonly used to treat lipid disorders in diabetic patients. Such drugs include, but are not limited to, HMG-CoA reductase inhibitors, nicotinic acid, bile acid sequestrants, and fibric acid derivatives. Polypeptides of the invention may also be used in combination with anti-hypertensive drugs, such as, for example, β-blockers, cathepsin S inhibitors and ACE inhibitors. Examples of β-blockers are: acebutolol, bisoprolol, esmolol, propanolol, atenolol, labetalol, carvedilol, and metoprolol. Examples of ACE inhibitors are: captopril, enalapril, lisinopril, benazepril, fosinopril, ramipril, quinapril, perindopril, trandolapril, and moexipril.

In a specific embodiment, the disease to be treated by administration of the pharmaceutical composition of the invention is selected from the group consisting of multiple sclerosis, type-I diabetes, Hashimoto's thyroiditis, Crohn's disease, rheumatoid arthritis, systemic lupus erythematosus (SLE), gastritis, autoimmune hepatitis, hemolytic anemia, autoimmune hemophilia, autoimmune lymphoproliferative syndrome (ALPS), autoimmune uveoretinitis, glomerulonephritis, Guillain-Barré syndrome, psoriasis, myasthenia gravis, autoimmune encephalomyelitis, Goodpasture's syndrome, Grave's disease, paraneoplastic pemphigus, autoimmune thrombocytopenic purpura, scleroderma with anti-collagen antibodies, mixed connective tissue disease, pernicious anemia, polymyositis, idiopathic Addison's disease, autoimmune-associated infertility, bullous pemphigoid, Sjogren's syndrome, idiopathic myxedema and colitis.

The invention further provides a kit comprising (i) a composition comprising a DSP composition or DNA delivery vehicle comprising DNA encoding DSPs and (ii) instructions for administering the composition to a subject in need thereof at intervals greater than 24 hours, more preferably greater than 36 hours, for the treatment of a disease, such as an autoimmune disease. In one embodiment, the autoimmune disorder is multiple sclerosis. In a preferred embodiment, the DSP composition is formulated in dosages for administration of greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any intervening interval thereof. In another embodiment of the kits described herein, the instructions indicate that the DSP is to be administered every about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or any interval in between. Kits may comprise additional components, such as packaging, instructions, and one or more apparatuses for the administration of the copolymer, such as a hypodermic syringe

V. Methods of Treatment

The instant invention provides for a further improvement on the need to improve the effectiveness of peptide immunotherapies. The improvement takes form in an ability to dynamically administer the compound based on the ability of the compound to achieve sustained chimerism, or immune regulation—either active or passive, while generating either a T_(H)1 immune posture, or a T_(H)2 immune posture, and while producing anti-compound antibodies at either a low or a high level. Dynamic administration of random sequence copolymer is comprised of any combination of dose, regimen, route of administration, and/or formulation. This dynamic immunomodulation provides for increased effectiveness at any of the multiple stages of a disease within a particular patient, as well as the ability to treat multiple, pathogenic antigenic-determinant unrelated diseases more effectively.

The invention provides methods for the treatment or prevention of a disease in a subject, preferably in a human, which subject is afflicted with or is suspected to be afflicted with the disease. Another embodiment of the present invention is a method for prophylactically treating a subject at risk of developing e.g., an autoimmune disease by administering a DSP composition. A subject at risk is identified by, for example, determining the genetic susceptibility to an autoimmune disease by testing for alleles of HLA that are associated with such autoimmune disease, and/or based on familial history, or other genetic markers that correlate with such autoimmune disease. Alternatively, the subject at risk is a subject that is scheduled to have or has had organ transplantation. Such prophylactic treatment may additionally comprise a DSP composition that binds to a second HLA molecule associated with the disease or condition to be treated. The second HLA molecule may be a HLA-DQ or HLA-DR molecule.

One aspect of the invention provides methods of treating or preventing a disease, the method comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the amelioration of a disease treatable with the DSP composition, said effective amount delivered to said subject at time intervals greater than 24 hours, 36 hours, or more preferably greater than 48 hours. A related aspect of the invention provides a method for the treatment of a subject in need thereof, comprising administering to said subject a dosing regimen of an effective amount of a DSP composition for the amelioration of a disease treatable with the DSP composition, said effective amount delivered to the subject using a sustained-release formulation which administers the DSP composition over a period of at least 2 days, at least 4 days, or at least 6 days, wherein the effective amount is an amount that is effective if delivered daily.

In a specific embodiment, the method of the invention is effective in treating a disease selected from the group consisting of multiple sclerosis, type-I diabetes, Hashimoto's thyroiditis, Crohn's disease, rheumatoid arthritis, systemic lupus erythematosus (SLE), gastritis, autoimmune hepatitis, hemolytic anemia, autoimmune hemophilia, autoimmune lymphoproliferative syndrome (ALPS), autoimmune uveoretinitis, glomerulonephritis, Guillain-Barré syndrome, psoriasis, myasthenia gravis, autoimmune encephalomyelitis, Goodpasture's syndrome, Grave's disease, paraneoplastic pemphigus, autoimmune thrombocytopenic purpura, scleroderma with anti-collagen antibodies, mixed connective tissue disease, pernicious anemia, polymyositis, idiopathic Addison's disease, autoimmune-associated infertility, bullous pemphigoid, Sjogren's syndrome, idiopathic myxedema and colitis.

In some embodiments, the disease of the methods of the present invention is mediated by T-cells, and in particular T_(H)1 cells or cells with T_(H)1 immune posture, or is a disease which is exacerbated by an excess of inflammatory cytokines. In one aspect the application relates to methods of modulating an immune response by administering a composition comprising a DSP composition as described above. In some embodiments, the disease include, without limitation, acute inflammation, rheumatoid arthritis, transplant rejection, asthma, inflammatory bowel disease, uveitis, restenosis, multiple sclerosis, psoriasis, wound healing, lupus erythematosus, allergies, atopic dermatitis, and neuroprotection and any other autoimmune or inflammatory disorder that can be recognized by one of ordinary skill in the art.

A preferred embodiment of the invention is a method for treating a disease treatable by administering to a subject in need thereof a composition comprising a DSP composition wherein the disease is selected from the group consisting of allergies, asthma, atopic dermatitis, and neuroprotection. The invention is not limited to any particular DSP composition or mode of administration.

One aspect of the invention provides methods of modulating the immune response for preventing, treating, or attenuating, Host versus Graft Disease (HVGD) or Graft versus Host Disease (GVHD), in the case of organ transplantation, and in preventing, treating, or attenuating autoimmune disorders, by administering a composition comprising a DSP composition as described above. Thus, in another aspect this application relates to methods of inducing sustained chimerism in case of organ transplantation. Additionally, the present application relates to methods of selectively inhibiting T-cell response to a graft, consequently, increasing the chances of survival of the graft.

Transplantation systems such as organ transplantations and bone marrow reconstitution have become important and effective therapies for many life threatening diseases. However, immune rejection is still the major barrier for successful transplantation. This is manifested in functional deterioration and graft rejection in the case of organ transplantation (host-versus-graft disease, or HVGD. Another manifestation of pathological immune reactivity is GVHD that occurs in approximately 30% of bone marrow recipients. Up to half of those patients who develop GVHD may succumb to this process. This high morbidity and mortality has led to continuous interest in the possibility of controlling or preventing GVHD. Clinicopathologically, two forms of GVHD have been recognized. Acute GVHD develops within the first 3 months after bone marrow transplantation and features disorders of skin, liver and gastrointestinal tract. Chronic GVHD is a multi-organ autoimmune-like disease emerging from 3 months up to 3 years post-transplantation and shares features common to naturally occurring autoimmune disorders, like systemic lupus erythematosus (SLE) and scleroderma. The methods described herein may be used to treat both acute and chronic GVHD.

In a specific embodiment of the methods described herein, the DSP composition based on applicable organ-derived or HLA-derived native peptide sequences may be used for prevention and treatment of GVHD in all cases of organ transplantation that develop GVHD. A particularly suitable application of the present invention is in allogeneic bone marrow transplantation. A treatment regimen may comprise administrations of the random copolymer at intervals greater than 24, 30, 36, 42, or 48 hours, for up to 60 days, starting from 2 days prior to the graft. Other immunosuppressive drugs, such as cyclosporine, methotrexate and prednisone, may be administered with the DSP composition.

The method of the invention may also be applied to the prevention and treatment of GVHD in the course of bone marrow transplantation in patients suffering from diseases curable by bone marrow transplantation, including leukemias, such as acute lymphoblastic leukemia (ALL), acute nonlymphoblastic leukemia (ANLL), acute myelocytic leukemia (AML) and chronic myelocytic leukemia (CML), severe combined immunodeficiency syndromes (SCID), osteopetrosis, aplastic anemia, Gaucher's disease, thalassemia and other congenital or genetically-determined hematopoietic or metabolic abnormalities.

One aspect of the invention is the administration of a DSP composition to a subject in need there of, as described above, in combination with other therapeutic agents that are effective in treating the conditions that are treated by administration of the DSP, or conditions that accompany or occur concurrently with the conditions that are treated by administration of the DSP. The additional therapeutically active agents may treat the same or related disease as the DSP composition, or may be intended to treat an undesirable side effect of administration of the DSP composition, such as to reduce swelling at a site of intradermal injection. Alternatively, the other therapeutic agents enhance the activity of DSP compositions. Such additional therapeutic agents are, by way of example, antibodies, cytokines, growth factors, enzyme inhibitors, antibiotics, antiviral agents, anti-inflammatory including steroids, immune boosters, antimetabolites, soluble cytokine receptors, and vitamin D or agents that increase the level of circulating vitamin D. Additional therapeutically active agents also include copolymers which bind to a HLA molecule associated with the disease such as Copolymer-1, or another DSP composition. The HLA molecule may be an HLA-DQ molecule or an HLA-DR molecule. The enzyme inhibitor may be a protease inhibitor or a cyclooxygenase inhibitor. Examples of the therapeutically active agents to be administered in conjunction with the DSP composition are recited in Section IV, “Pharmaceutical Composition” section, though the administration of these agents are not limited to co-administration as a single composition. The additional therapeutic agents may be administered before, concomitantly with, or after the administration of the DSP composition, at such time that the effect of the additional therapeutic agents and the effect of the DSP composition overlap at some time point.

In particular, the method of present invention further comprises administering to said subject an anti-lymphocyte therapies. In such embodiments, the DSP composition of the present invention are administered to a patient with an autoimmune disease following an anti-lymphocyte therapy (e.g., anti-T cell or anti-B cell). In one embodiment, anti-T cell therapies may use antibodies, such as Campath-1H® (alemtuzumab; anti-CD52), OKT3 (anti-CD3), thymoglobulin (anti-thymocytic globulins), or anti-IL2R antibodies (e.g., daclizumab and basiliximab). Alternatively, anti-T cell therapies may use chemotherapy agents such as fludarabine, external-beam radiation therapy (XRT), and cyclophosphamide. In one embodiment, the anti-lymphocyte therapy agent selected from the group consisting of a polyclonal antibody or a monoclonal antibody. In certain embodiments, the polyclonal antibody is antithymocyte gamma globulin (ATGAM). In other embodiment, the antibody is a monoclonal antibody selected from the group consisting of alemtuzumab (Campath®), muromonab (OKT®3), daclizumab, and basiliximab. In another embodiment, the method of the invention comprises administering to said subject an anti B-cell therapy. In one embodiment, the anti-B-cell therapy anti CD-20 antibody such as the antibody Rituxan (Rituximab). The dosage of the above additional treatments to be administered to a subject varies with the precise nature of the condition being treated and the recipient of the treatment. The scaling of dosages for human administration can be performed according to art-accepted practices. For example, the dose for Campath-1H® will generally be in the range 1 to about 100 mg for an adult patient, usually administered daily for a period between 1 and 30 days. The preferred daily dose is 1 to 10 mg per day although in some instances larger doses of up to 40 mg per day may be used (see, e.g., U.S. Pat. No. 6,120,766). Although not wishing to be bound by any particular mechanism or theory, it is believed that such combination therapy can enhance the therapeutic efficacy without any potential long-term toxicity. To illustrate, Campath-1H® is introduced in a patient for initial induction immunosuppression. Then, the patient is administered a copolymer of the present invention in the absence of Campath-1H®

In a preferred embodiment, the DSP composition of the present invention can be administered with a form of vitamin D that is or becomes biologically active within the body of the subject receiving such form of vitamin D. The classical role of vitamin D that of an involvement in the regulation of calcium homeostasis. After the discovery of a vitamin D receptor (VDR) on peripheral blood mononuclear cells, interest in its role in the etiopathogenesis of certain autoimmune diseases increased. Vitamin D deficiency has been shown in increase susceptibility to experimental models of multiple sclerosis (MS), while vitamin D treatment suppressed these experimental models of MS. Further studies have shown that limiting the VDR signaling on T cells increases Th1 effector cells, while augmenting VDR signaling increases T regulatory cells. Thus, any increase in Vitamin D during the course of immunomodulatory therapy, such as those described herein, would have a potentially synergistic effect leading to increased efficacy of treatment as the vitamin D will assist in increasing the regulatory component of the treatment, while the peptide based immunotherapy will provide an epitope specific direction to the adaptive immune response

In particular, for the role vitamin D plays in immunological phenomena, see M. T. Cantorna, Progress in Biophys. Molec. Biol. 2006 September; 92(1):60-4. Epub 2006 Feb. 28.) and Spach and Hayes, J. Immunol. 2005, 175:4199-4126.

In one embodiment of the methods described herein, the route of administration can be oral, intraperitoneal, transdermal, subcutaneous, by intravenous or intramuscular injection, by inhalation, topical, intralesional, or by infusion; liposome-mediated delivery; intrathecal, gingival pocket, rectal, intravaginal, intrabronchial, nasal, transmucosal, intestinal, ocular or otic delivery, or any other methods known in the art as one skilled in the art may easily perceive. Administration can be systemic or local. In the event more than one DSP composition is being administered to a subject during the same or overlapping time period, such additional therapeutic agent may be administered by a route different from that for the administration of the DSP composition.

In general, an embodiment of the invention is to administer a suitable dose of a therapeutic DSP composition that will be the lowest effective dose to produce a therapeutic effect, for example, mitigating symptoms. The therapeutic DSP compositions are preferably administered at a dose per subject, which corresponds to a dose per day of at least about 2 mg, at least about 5 mg, at least about 10 mg, or at least about 20 mg as appropriate minimal starting dosages, or about x mg, wherein x is an integer between 1 and 20. In one embodiment of the methods described herein, a dose of about 0.01 to about 500 mg/kg can be administered. In general, the effective dosage of the DSP composition of the present invention is about 50 to about 400 micrograms of the composition per kilogram of the subject per day. In one specific embodiment, the equivalent dosage per day, regardless of the frequency with which the doses are administered, is from about 5 to 100, or more preferably, from about 10 to 40, or more preferably about 20 mg/day. In another specific embodiment, each individual dosage in the treatment regimen is from about 5 to 100, or more preferably from about 10 to 40, or more preferably about 20 mg/dose.

However, it is understood by one skilled in the art that the dose of the DSP composition of the invention will vary depending on the subject and upon the particular route of administration used. It is routine in the art to adjust the dosage to suit the individual subjects. Additionally, the effective amount may be based upon, among other things, the size of the DSPs, the biodegradability of the DSPs, the bioactivity of the DSPs and the bioavailability of the DSPs. If the DSPs does not degrade quickly, such as is expected when the DSPs comprise unnatural amino acids or are peptidomimetics, is bioavailable and highly active, a smaller amount will be required to be effective. The actual dosage suitable for a subject can easily be determined as a routine practice by one skilled in the art, for example a physician or a veterinarian given a general starting point. For example, the physician or veterinarian could start doses of the DSP composition of the invention employed in the pharmaceutical composition at a level lower than that required in order to achieve the desired therapeutic effect, and increase the dosage with time until the desired effect is achieved. The dosage of the DSP composition may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disorder or disease state is observed, or if the disorder or disease state has been ablated, or if an unacceptable side effects are seen with the starting dosage.

In one embodiment, a therapeutically effective amount of the DSP composition is administered to the subject in a treatment regimen comprising intervals of at least 36 hours, or more preferably 48 hours, between dosages. In another embodiment, the DSP composition is administered at intervals of at least 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days. In some embodiments, the DSP composition is administered every other day, while in other embodiments it is administered weekly. If two different DSP compositions, or DSP composition with another therapeutic agent, are administered to the subject, such administration may take place at the same time, such as simultaneously, or essentially at the same time, such as in succession. Alternatively, their administration may be staggered. For example, two DSP compositions which are each administered every 48 hours may both be administered on the same days, or one may be administered one day and the other on the next day and so on in an alternating fashion.

Treatment regimens with longer dosing intervals, consequently often with lower total exposure of DSPs, are expected to induce lower titers of antibodies against DSPs themselves, while still inducing desired protective effects. Such reduction of neutralizing antibodies are desirable because it is considered likely to help DSP compositions to retain its effectiveness without being neutralized, and it is associated with reduced risk of anaphylactic shocks, providing safer treatments of diseases. Longer interval regimens are also desirable in treatment of some of the diseases, because they strengthen the bias for T_(H)2 responses, which is considered to be the mode of action for the treatment of these diseases by DSPs.

In other embodiments, the DSP composition is administered in a treatment regimen which comprises at least one uneven time interval, wherein at least one of the time intervals is at least 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or the equivalent amount of days.

In one embodiment, the DSP composition is administered to be subject at least three times during a treatment regimen, such that there are at least two time intervals between administrations. These intervals may be denoted I₁ and I₂. If the DSP composition is administered four times, then there would be an additional interval between the third and fourth administrations, I₃, such that the number of intervals for a given number “n” of administrations is n−1. Accordingly, in one embodiment, at least one of the time intervals between administrations is greater than about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours. In another embodiment, at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the total number n−1 of time intervals are at least about 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours.

In yet another embodiment, the average time interval between administrations ((I₁+I₂+ . . . +I_(n-1))/n−1) is at least 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 96, 102, 108, 114, 120, 126, 132, 138, 144, 150, 156, 162, 168, 174, 180, 186, 192, 198, 204, 210, 216, 222, 228, 234, or 240 hours, or at least two weeks.

In another embodiment, the dosage regimen consists of two or more different interval sets. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg copolymer/m² body surface area of the subject, wherein the subject is a human. In some embodiment of the invention, the dosing regimen starts with dosing the subject every other day, every third day, weekly, biweekly, or monthly. The dosage for administration every other day or every third day may be up to about 65 mg/m² and 110 mg/m² respectively. For a dosing regimen comprising dosing of the random copolymer every week, the dose comprises up to about 500 mg/m², and for a dosing regimen comprising dosing of the random copolymer every two weeks or every month, up to 1.5 g/m² may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 500 mg/m² body surface area weekly, up to maximum of about 1.5 g/m² body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m² body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

In other embodiments of the invention, any of the methods of the invention may be practiced using sustained release formulation comprising a DSP composition. When administering a DSP composition of the invention using a sustained release formula, the overall exposure to the DSP is generally lower than in bolus administration. For example, a first part of the dosage regimen is administered to a subject daily, every other day, or every third day, for example, at about 22 mg DSP/m² body surface area of the subject, wherein the subject is a human. In some embodiment of the invention, the dosing regimen uses sustained release formula, dosing the subject every other day, every third day, weekly, biweekly, or monthly so that the copolymer is released during the interval. The dosage for administration every other day or every third day may be up to about 35 mg/m² and 65 mg/m² respectively. For a dosing regimen comprising dosing of the DSP composition every week, the dose comprises up to about 140 mg/m², and for a dosing regimen comprising dosing of the DSP composition every two weeks or every month, up to 750 mg/m² may be administered. The first part of the dosing regimen may be administered for up to 30 days, for example, 7, 14, 21, or 30 days. A subsequent second part of the dosing regimen with a different, longer interval administration with usually lower exposure (step-down dosage), administered weekly, every 14 days, or monthly may optionally follow, for example, at 140 mg/m² body surface area weekly, up to maximum of about 1.5 g/m² body surface area, continuing for 4 weeks up to two years, for example, 4, 6, 8, 12, 16, 26, 32, 40, 52, 63, 68, 78, or 104 weeks. Alternatively, if the disease goes into remission or generally improves, the dosage may be maintained or kept at lower than maximum amount, for example, at 140 mg/m² body surface area weekly. If, during the step-down dosage regimen, the disease condition relapses, the first dosage regimen may be resumed until effect is seen, and the second dosing regimen may be implemented. This cycle may be repeated multiple times as necessary.

For such sustained release administration, such method comprises applying a sustained-release transdermal patch or implanting a sustained-release capsule or a coated implantable medical device so that a therapeutically effective dose of the copolymer of the present invention is delivered at defined time intervals to a subject of such a method. The DSP composition of the subject invention may be delivered via a capsule which allows regulated-release of the DSPs over a period of time. Controlled or sustained-release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils). Also comprehended by the invention are particulate compositions coated with polymers (e.g., poloxamers or poloxamines). In certain embodiments, a source of a DSP composition is stereotactically provided within or proximate to the area of autoimmune attack, for example, near the pancreas for the treatment of IDDM.

An improvement in the symptoms of a subject afflicted with a disease as a result of administration of the DSP composition may be noted by a decrease in frequency of recurrences of episodes of the disease symptoms, by decrease in severity of symptoms, and by elimination of recurrent episodes for a period of time after the start of administration. A therapeutically effective dosage preferably reduces symptoms and frequency of recurrences by at least about 20%, for example, by at least about 40%, by at least about 60%, and by at least about 80%, or by about 100% elimination of one or more symptoms, or elimination of recurrences of the autoimmune disease, relative to untreated subjects. The period of time can be at least about one month, at least about six months, or at least about one year.

For example, an improvement in the symptoms of a subject afflicted with arthritis or any other autoimmune disorder which results in inflammation of the joints may be noted by a reduction in edema of one or more joints, by a reduction in inflammation in one or more joints, or by an increase in mobility in one or more joints. A therapeutically effective dosage preferably reduces joint inflammation and edema and improves mobility by at least about 20%, more preferably by at least about 40%, even more preferably by at least about 60%, and even still more preferably by at least about 80%, relative to untreated subjects.

DEFINITIONS

The term “associated with” means “coexistent with” or “in correlation with.” The term does not necessarily indicate causal relationship, though such relationship may exist.

The term “binding” refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions, and including interactions such as salt bridges and water bridges.

The term “HLA molecule” means any class II major histocompatibility complex glycoproteins.

The term “immunomodulation” means the process of increasing or decreasing the immune system's ability to mount a response against a particular antigenic determinant through the T-cell receptor (“TCR”)'s recognition of complexes formed by major histocompatibility complex (“MHC”) and antigens.

The term “immunosuppression” means the depression of immune response and reactivity in recipients of organ or bone marrow allotransplants.

The term “MHC activity” refers to the ability of an MHC molecule to stimulate an immune response, e.g., by activating T cells. An inhibitor of MHC activity is capable of suppressing this activity, and thus inhibits the activation of T cells by MHC. In preferred embodiments, a subject inhibitor selectively inhibits activation by a particular class II MHC isotype or allotype. Such inhibitors may be capable of suppressing a particular undesirable MHC activity without interfering with all MHC activity in an organism, thereby selectively treating an unwanted immune response in an animal, such as a mammal, preferably a human, without compromising the animal's immune response in general.

The term “organ-specific protein” or “organ-specific antigen” means proteins that are expressed predominantly or exclusively by cells comprising a certain organ.

The term “patient” refers to an animal, preferably a mammal, including humans as well as livestock and other veterinary subjects.

The terms “peptide”, “polypeptide” and “protein” are used interchangeably herein. These terms refer to unmodified amino acid chains, and also include minor modifications, such as phosphorylations, glycosylations and lipid modifications. The terms “peptide” and “peptidomimetic” are not mutually exclusive and include substantial overlap.

A “peptidomimetic” includes any modified form of an amino acid chain, such as a phosphorylation, capping, fatty acid modification and including unnatural backbone and/or side chain structures. As described below, a peptidomimetic comprises the structural continuum between an amino acid chain and a non-peptide small molecule. Peptidomimetics generally retain a recognizable peptide-like polymer unit structure. Thus, a peptidomimetic may retain the function of binding to a HLA protein forming a complex which activates autoreactive T cells in a patient suffering from an autoimmune disease.

The term “amino acid residue” is known in the art. In general the abbreviations used herein for designating the amino acids and the protective groups are based on recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature (see Biochemistry (1972) 11:1726-1732). In certain embodiments, the amino acids used in the application of this invention are those naturally occurring amino acids found in proteins, or the naturally occurring anabolic or catabolic products of such amino acids which contain amino and carboxyl groups. Particularly suitable amino acid side chains include side chains selected from those of the following amino acids: glycine, alanine, valine, cysteine, leucine, isoleucine, serine, threonine, methionine, glutamic acid, aspartic acid, glutamine, asparagine, lysine, arginine, proline, histidine, phenylalanine, tyrosine, and tryptophan.

The term “amino acid residue” further includes analogs, derivatives and congeners of any specific amino acid referred to herein, as well as C-terminal or N-terminal protected amino acid derivatives (e.g. modified with an N-terminal or C-terminal protecting group). For example, the present invention contemplates the use of amino acid analogs wherein a side chain is lengthened or shortened while still providing a carboxyl, amino or other reactive precursor functional group for cyclization, as well as amino acid analogs having variant side chains with appropriate functional groups). For instance, the subject compound can include an amino acid analog such as, for example, cyanoalanine, canavanine, djenkolic acid, norleucine, 3-phosphoserine, homoserine, dihydroxy-phenylalanine, 5-hydroxytryptophan, 1-methylhistidine, 3-methylhistidine, diaminopimelic acid, ornithine, or diaminobutyric acid. Other naturally occurring amino acid metabolites or precursors having side chains which are suitable herein will be recognized by those skilled in the art and are included in the scope of the present invention.

Most of the amino acids used in the DSPs of the present invention may exist in particular geometric or stereoisomeric forms. In preferred embodiments, the amino acids used to form the subject DSPs are (L)-isomers, although (D)-isomers may be included in the DSPs such as at non-anchor positions or in the case of peptidomimetic versions of the DSPs.

“Prevent”, as used herein, means to delay or preclude the onset of, for example, one or more symptoms, of a disorder or condition.

“Treat”, as used herein, means at least lessening the severity or ameliorating the effects of, for example, one or more symptoms, of a disorder or condition.

“Treatment regimen” as used herein, encompasses therapeutic, palliative and prophylactic modalities of administration of one or more compositions comprising one or more DSP compositions. A particular treatment regimen may last for a period of time at a particular dosing pattern, which will vary depending upon the nature of the particular disease or disorder, its severity and the overall condition of the patient, and may extend from once daily, or more preferably once every 36 hours or 48 hours or longer, to once every month or several months.

The terms “structure-activity relationship” or “SAR” refer to the way in which altering the molecular structure of drugs alters their interaction with a receptor, enzyme, etc.

The practice of the present invention will employ, where appropriate and unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, virology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are described in the literature. See, for example, Molecular Cloning: A Laboratory Manual, 3rd Ed., ed. by Sambrook and Russell (Cold Spring Harbor Laboratory Press: 2001); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Using Antibodies, Second Edition by Harlow and Lane, Cold Spring Harbor Press, New York, 1999; Current Protocols in Cell Biology, ed. by Bonifacino, Dasso, Lippincott-Schwartz, Harford, and Yamada, John Wiley and Sons, Inc., New York, 1999; and PCR Protocols, ed. by Bartlett et al., Humana Press, 2003; PHARMACOLOGY A Pathophysiologic Approach Edited by Josehp T. DiPiro, Robert Talbert, Gary, Yee, Gary Matzke, Barbara Wells, and L. Michael Posey. 5th edition 2002 McGraw Hill; Pathologic Basis of Disease. Ramzi Cotran, Vinay Kumar, Tucker Collins. 6th Edition 1999. Saunders.

Example 1 Preparation of a DSP Composition from Fictitious Base Peptides

For ease of understanding, as an illustration, preparation of a DSP composition deriving from two fictitious peptide sequences, representing a known epitope, is described and shown in the table depicted in FIG. 6. In this illustration, the cassettes consist of five amino acids each, (x1, x2, x3, x4, x5=THMCE (SEQ ID NO: 237) in y₁ and PWKNA (SEQ ID NO: 238) in y₂). THMCE (SEQ ID NO: 237) is defined as having an input ratio of a=7, b=1, c=1, d=1, e=10. PWKNA (SEQ ID NO: 238) is defined as having an input ratio of a=1, b=3, c=3, d=3, e=20. For synthesis, the identity of group of amino acids occupying each amino acid position for each peptide is determined using the preferred method of amino acid substitution described by Kosiol et al., J. Theoretical Biol. 228:97-106, 2004, as shown in FIG. 4 (or less preferably an equivalent means of systematically altering amino acids), and the overall ratio of amino acids that occupy each of such positions in the resulting collective DSP composition is given above. Each cassette, y₁ and y₂, will twice be repeated two times, generating an order of y₁ y₁ y₂ y₂ y₁ y₁ y₂ y₂. N_(n) are the number of times the sequence within the cassette is to be repeated, and in our fictitious example N=2. MN can be any type of modifying moiety. MN must be amenable to solid phase synthesis methods. For this fictitious example, a modifying moiety of amino acids that would target the DSP to a certain location within a subject is chosen, such as an RGD-based sequence motif on a particular integrin such as alphaVbeta3. In this example the C-terminal modifier will also be an RGD-based motif, but comprised of D-amino acids.

The DSP composition as described above is prepared using a solid phase peptide synthesis method as described elsewhere in this disclosure.

Example 2 Preparation of a DSP Composition from MBP(83-99)

Myelin basic protein is implicated in the pathology of multiple sclerosis, and several epitopes have been identified and proven to be relevant in the disease symptoms and progression. One such epitope spans amino acid residues 83 to 99 of myelin basic protein (MBP(83-99). COP-1 is thought to target the same binding pocket of HLA as MBP(83-99) does. A DSP composition is defined and prepared using MBP (83-99) as the base peptide sequence.

The methods and rules to define the identity of amino acids for each position of the resulting peptides are described above in Example 1. The actual application of such rules are illustrated in the tables of FIG. 8A-B. As with Example 1, the DSP composition is synthesized using a solid phase peptide synthesis method.

The following references are exemplary sources of epitopes useful as base peptide sequences. Numbers to the left are the reference numbers of Table I.

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The contents of any patents, patent applications, patent publications, or scientific articles referenced anywhere in this application are herein incorporated in their entirety.

Sequence Listings in addition to Table I SEQ ID NO: 190 HSP-60 (human): MLRLPTVFRQ MRPVSRVLAP HLTRAYAKDV KFGADARALM LQGVDLLADA VAVTMGPKGR TVIIEQSWGS PKVTKDGVTV AKSIDLKDKY KNIGAKLVQD VANNTNEEAG DGTTTATVLA RSIAKEGFEK ISKGANPVEI RRGVMLAVDA VIAELKKQSK PVTTPEEIAQ VATISANGDK EIGNIISDAM KKVGRKGVIT VKDGKTLNDE LEIIEGMKFD RGYISPYFIN TSKGQKCEFQ DAYVLLSEKK ISSIQSIVPA LEIANAHRKP LVIIAEDVDG EALSTLVLNR LKVGLQVVAV KAPGFGDNRK NQLKDMAIAT GGAVFGEEGL TLNLEDVQPH DLGKVGEVIV TKDDANLLKG KGDKAQIEKR IQEIIEQLDV TTSEYEKEKL NERLAKLSDG VAVLKVGGTS DVEVNEKKDR VTDALNATRA AVEEGIVLGG GCALLRCIPA LDSLTPANED QKIGIEIIKR TLKIPAMTIA KNAGVEGSLI VEKIMQSSSE VGYDAMAGDF VNMVEKGIID PTKVVRTALL DAAGVASLLT TAEVVVTEIP KEEKDPGMGA MGGMGGGMGG GMF SEQ ID NO: 191 HSP-70 (human): MAKAAAIGID LGTTYSCVGV FQHGKVEIIA NDQGNRTTPS YVAFTDTERL IGDAAKNQVA LNPQNTVFDA KRLIGRKFGD PVVQSDMKHW PFQVINDGDK PKVQVSYKGE TKAFYPEEIS SMVLTKMKEI AEAYLGYPVT NAVITVPAYF NDSQRQATKD AGVIAGLNVL RIINEPTAAA IAYGLDRTGK GERNVLIFDL GGGTFDVSIL TIDDGIFEVK ATAGDTHLGG EDFDNRLVNH FVEEFKRKHK KDISQNKRAV RRLRTACERA KRTLSSSTQA SLEIDSLFEG IDFYTSITRA RFEELCSDLF RSTLEPVEKA LRDAKLDKAQ IHDLVLVGGS TRIPKVQKLL QDFFNGRDLN KSINPDEAVA YGAAVQAAIL MGDKSENVQD LLLLDVAPLS LGLETAGGVM TALIKRNSTI PTKQTQIFTT YSDNQPGVLI QVYEGERAMT KDNNLLGRFE LSGIPPAPRG VPQIEVTFDI DANGILNVTA TDKSTGKANK ITITNDKGRL SKEEIERMVQ EAEKYKAEDE VQRERVSAKN ALESYAFNMK SAVEDEGLKG KISEADKKKV LDKCQEVISW LDANTLAEKD EFEHKRKELE QVCNPIISGL YQGAGGPGPG GFGAQGPKGG SGSGPTIEEV D SEQ ID NO: 192 HSP-90 alpha (human): PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLTI VDTGIGMTKA DLINNLGTIA KSGTKAFMEA LQAGADISMI GQFGVGFYSA YLVAEKVTVI TKHNDDEQYA WESSAGGSFT VRTDTGEPMG RGTKVILHLK EDQTEYLEER RIKEIVKKHS QFIGYPITLF VEKERDKEVS DDEAEEKEDK EEEKEKEEKE SEDKPEIEDV GSDEEEEKKD GDKKKKKKIK EKYIDQEELN KTKPIWTRNP DDITNEEYGE FYKSLTNDWE DHLAVKHFSV EGQLEFRALL FVPRRAPFDL FENRKKKNNI KLYVRRVFIM DNCEELIPEY LNFIRGVVDS EDLPLNISRE MLQQSKILKV IRKNLVKKCL ELFTELAEDK ENYKKFYEQF SKNIKLGIHE DSQNRKKLSE LLRYYTSASG DEMVSLKDYC TRMKENQKHI YYITGETKDQ VANSAFVERL RKHGLEVIYM IEPIDEYCVQ QLKEFEGKTL VSVTKEGLEL PEDEEEKKKQ EEKKTKFENL CKIMKDILEK KVEKVVVSNR LVTSPCCIVT STYGWTANME RIMKAQALRD NSTMGYMAAK KHLEINPDHS IIETLRQKAE ADKNDKSVKD LVILLYETAL LSSGFSLEDP QTHANRIYRM IKLGLGIDED DPTADDTSAA VTEEMPPLEG DDDTSRMEEV D SEQ ID NO: 193 HSP-90 beta (human): PEEVHHGEEE VETFAFQAEI AQLMSLIINT FYSNKEIFLR ELISNASDAL DKIRYESLTD PSKLDSGKEL KIDIIPNPQE RTLTLVDTGI GMTKADLINN LGTIAKSGTK AFMEALQAGA DISMIGQFGV GFYSAYLVAE KVVVITKHND DEQYAWESSA GGSFTVRADH GEPIGRGTKV ILHLKEDQTE YLEERRVKEV VKKHSQFIGY PITLYLEKER EKEISDDEAE EEKGEKEEED KDDEEKPKIE DVGSDEEDDS GKDKKKKTKK IKEKYIDQEE LNKTKPIWTR NPDDITQEEY GEFYKSLTND WEDHLAVKHF SVEGQLEFRA LLFIPRRAPF DLFENKKKKN NIKLYVRRVF IMDSCDELIP EYLNFIRGVV DSEDLPLNIS REMLQQSKIL KVIRKNIVKK CLELFSELAE DKENYKKFYE AFSKNLKLGI HEDSTNRRRL SELLRYHTSQ SGDEMTSLSE YVSRMKETQK SIYYITGESK EQVANSAFVE RVRKRGFEVV YMTEPIDEYC VQQLKEFDGK SLVSVTKEGL ELPEDEEEKK KMEESKAKFE NLCKLMKEIL DKKVEKVTIS NRLVSSPCCI VTSTYGWTAN MERIMKAQAL RDNSTMGYMM AKKHLEINPD HPIVETLRQK AEADKNDKAV KDLVVLLFET ALLSSGFSLE DPQTHSNRIY RMIKLGLGID EDEVAAEEPN AAVPDEIPPL EGDEDASRME EVD SEQ ID NO: 194 GAD65 (human) MASPGSGFWS FGSEDGSGDS ENPGTARAWC QVAQKFTGGI GNKLCALLYG DAEKPAESGG SQPPRAAARK AACACDQKPC SCSKVDVNYA FLHATDLLPA CDGERPTLAF LQDVMNILLQ YVVKSFDRST KVIDFHYPNE LLQEYNWELA DQPQNLEEIL MHCQTTLKYA IKTGHPRYFN QLSTGLDMVG LAADWLTSTA NTNMFTYEIA PVFVLLEYVT LKKMRETTGW PGGSGDGIFS PGGAISNMYA MMIARFKMFP EVKEKGMAAL PRLIAFTSEH SHFSLKKGAA ALGIGTDSVI LIKCDERGKM IPSDLERRIL EAKQKGFVPF LVSATAGTTV YGAFDPLLAV ADICKKYKIW MHVDAAWGGG LLMSRKHKWK LSGVERANSV TWNPHKMMGV PLQCSALLVR EEGLMQNCNQ MHASYLFQQD KHYDLSYDTG DKALQCGRHV DVFKLWLMWR AKGTTGFEAH VDKCLELAEY LYNIIKNREG YEMVFDGKPQ HTNVCFWYIP PSLRTLEDNE ERMSRLSKVA PVIKARNMEY GTTMVSYQPL GDKVNFFRMV ISNPAATHQD IDELIEEIER LGQDL SEQ ID NO: 195 Ro60 (human) MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQE PMLFALAICS QCSDISTKQA AFKAVSEVCR IPTHLFTFIQ FKKDLKESMK CGMWGRALRK AIADWYNEKG GMALALAVTK YKQRNGWSHK DLLRLSHLKP SSEGLAIVTK YITKGWKEVH ELYKEKALSV ETEKLLKYLE AVEKVKRTRD ELEVIHLIEE HRLVREHLLT NHLKSKEVWK ALLQEMPLTA LLRNLGKMTA NSVLEPGNSE VSLVCEKLCN EKLLKKARIH PFHILTALET YKTGHGLRGK LKWRPDEEIL KALDAAFYKT FKTVEPTGKR FLLAVDVSAS MNQRVLGSIL NASTVAAAMC MVVTRTEKDS YVVAFSDEMV PCPVTTDMTL QQVLMAMSQI PAGGTDCSLP MIWAQKTNTP ADVFIVFTDN ETFAGGVHPA IALREYRKKM DIPAKLIVCG MTSNGFTIAD PDDRALQNTL LNKSF SEQ ID NO: 196 HLA DQ2 ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYTHEFDGDE QFYVDLGRKE TVWCLPELRQ FRGFDPQFAL TNIAVLKHNL NSLIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLTNGHSVTE GVSETTFLSK SDHSFFKISY LTLLPSAEES YDCKVEHWGL DKPLLKHWEP E SEQ ID NO: 197 HLA DQ2 BETA CHAIN SPEDEVYQFK GMCYFTNGTE RVRLVSRSIY NREEIVRFDS DVGEFRAVTL LGLPAAEYWN SQKDILERKR AAVDRVCRHN YQLELRTTLQ RRVEPTVTIS PSRTEALNHH NLLVCSVTDF YPAQIKVRWF RKDQEETAGV VSTPLIRNGD WTFQILVMLE MTPQRGDVYT CHVEHPSLQS PITVEWRAQS SEQ ID NO: 198 HLA DQ7 ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYTHEFDGDE QFYVDLGRKE TVWCLPELRQ FRGFDPQFAL TNIAVLKHNL NSLIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLTNGHSVTE GVSETTFLSK SDHSFFKISY LTLLPSAEES YDCKVEHWGL DKPLLKHWEP E SEQ ID NO: 199 HLA DQ7 BETA CHAIN SPEDFVYQFK AMCYFTNGTE RVYVTRYIYN REEYARFDSD VEVYRAVTPL GPPDAEYWNS QKEVLERTRA ELDTVCRHNY QLELRTTLQR RVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETTGVV STPLIRNGDW TFQILVMLEM TPQHGDVYTC HVEHPSLQNP ITVEWRAQS SEQ ID NO: 200 HLA DQS ALPHA CHAIN VADHVASYGV NLYQSYGPSG QYSHEFDGDE EFYVDLERKE TVWQLPLFRR FRRFDPQFAL TNIAVLKHNL NIVIKRSNST AATNEVPEVT VFSKSPVTLG QPNTLICLVD NIFPPVVNIT WLSNGHSVTE GVSETSFLSK SDHSFFKISY LTFLPSDDEI YDCKVEHWGL DEPLLKHWEP E SEQ ID NO: 201 HLA DQ8 BETA CHAIN SPEDFVYQFK GMCYFTNGTE RVRLVTRYIY NREEYARFDS DVGVYRAVTP LGPPAAEYWN SQKEVLERTR AELDTVCRHN YQLELRTTLQ RRVEPTVTIS PSRTEALNHH NLLVCSVTDF YPAQIKVRWF RNDQEETTAG VVSTPLIRNG DWTFQILVML EMTPQRGDVY TCHVEHPSLQ NPIIVEWRAQ S SEQ ID NO: 202 Human myelin oligodendrocyte glycoprotein (MOG) QFRVIGPRHP IRALVGDEVE LPCRISPGKN ATGMEVGWYR PPFSRVVHLY RNGKDQDGDQ APEYRGRTEL LKDAIGEGKV TLRIRNVRFS DEGGFTCFFR DHSYQEEAAM ELKVEDPFYW VSPGVLVLLA VLPVLLLQIT VGLVFLCLQY RLRGKLRAEI ENLHRTFGQF LEELRNPF SEQ ID NO: 203 Human Myelin-associated oligodendrocyte basic protein MSQKPAKEGP RLSKNQKYSE HFSIHCCPPF TFLNSKKEIV DRKYSICKSG CFYQKKEEDW ICCACQKTRL KRKIRPTPKK K SEQ ID NO: 204 HUMAN DESMOGLEIN 3 PREPROPROTEIN MMGLFPRTTG ALAIFVVVIL VHGELRIETK GQYDEEEMTM QQAKRRQKRE WVKFAKPCRE GEDNSKRNPI AKITSDYQAT QKITYRISGV GIDQPPFGIF VVDKNTGDIN ITAIVDREET PSFLITCRAL NAQGLDVEKP LILTVKILDI NDNPPVFSQQ IFMGEIEENS ASNSLVMILN ATDADEPNHL NSKIAFKIVS QEPAGTPMFL LSRNTGEVRT LTNSLDREQA SSYRLVVSGA DKDGEGLSTQ CECNIKVKDV NDNFPMFRDS QYSARIEENI LSSELLRFQV TDLDEEYTDN WLAVYFFTSG NEGNWFEIQT DPRTNEGILK VVKALDYEQL QSVKLSIAVK NKAEFHQSVI SRYRVQSTPV TIQVINVREG IAFRPASKTF TVQKGISSKK LVDYILGTYQ AIDEDTNKAA SNVKYVMGRN DGGYLMIDSK TAEIKFVKNM NRDSTFIVNK TITAEVLAID EYTGKTSTGT VYVRVPDFND NCPTAVLEKD AVCSSSPSVV VSARTLNNRY TGPYTFALED QPVKLPAVWS ITTLNATSAL LRAQEQIPPG VYHISLVLTD SQNNRCEMPR SLTLEVCQCD NRGICGTSYP TTSPGTRYGR PHSGRLGPAA IGLLLLGLLL LLLAPLLLLT CDCGAGSTGG VTGGFIPVPD GSEGTIHQWG IEGAHPEDKE ITNICVPPVT ANGADFMESS EVCTNTYARG TAVEGTSGME MTTKLGAATE SGGAAGFATG TVSGAASGFG AATGVGICSS GQSGTMRTRH STGGTNKDYA DGAISMNFLD SYFSQKAFAC AEEDDGQEAN DCLLIYDNEG ADATGSPVGS VGCCSFIADD LDDSFLDSLG PKFKKLAEIS LGVDGEGKEV QPPSKDSGYG IESCGHPIEV QQTGFVKCQT LSGSQGASAL STSGSVQPAV SIPDPLQHGN YLVTETYSAS GSLVQPSTAG FDPLLTQNVI VTERVICPIS SVPGNLAGPT QLRGSHTMLC TEDPCSRLI 

1. A process for manufacturing a composition comprising directed sequence polymers (DSPs), comprising the steps of: (1) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with an autoimmune disease; (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, each cassette having a sequence of amino acid positions corresponding to each amino acid of the base peptide sequence, wherein, for at least one amino acid position of the first cassette of the directed sequence polymers, an amino acid is added, said amino acid randomly selected from a mixture of amino acids comprising the original amino acid found at that amino acid position, alanine (A), and, optionally, at least one conserved substitution, wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid concentration of the DSPs; (3) optionally extending the length of the DSPs by at least one of (a) repeating step (2) for 2 to 15 cycles and elongating the DSP under the same condition; or (b) repeating step (2) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; or (c) repeating steps (1) and (2) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; or (d) assembling 2 to 15 cassettes synthesized in a single cycle of step (2); or (e) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (2), and second and more cassettes synthesized under other conditions of step (2); (4) optionally further elongating the DSPs by repeating steps (2) and (3) for 2 to 15 cycles, wherein for each cycle a new cassette of the DSP is designed independently from any of the previous cassettes designated by previous cycles of step (2); wherein the number of cycles selected in steps (3) and (4) is selected so that the final length of the DSP is about 25 to 300 amino acid residues.
 2. The process according to claim 1, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 1 through 189 depicted in Table I.
 3. The process according to claim 1, wherein the autoimmune disease is selected from multiple sclerosis, systemic lupus erythematosus, type I diabetes mellitus, myasthenia gravis, rheumatoid arthritis, and pemphigus vulgaris.
 4. The process according to claim 3, wherein the autoimmune disease is multiple sclerosis.
 5. The process according to claim 3, wherein the autoimmune disease is systemic lupus erythematosus.
 6. The process according to claim 3, wherein the autoimmune disease is type I diabetes mellitus.
 7. The process according to claim 3, wherein the autoimmune disease is myasthenia gravis.
 8. The process according to claim 3, wherein the autoimmune disease is rheumatoid arthritis.
 9. The process according to claim 3, wherein the autoimmune disease is pemphigus vulgaris.
 10. The process according to claim 4, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from osteopontin, an HLA protein, myelin oligodendrite glycoprotein, myelin basic protein (MBP), proteolipid protein, and myelin associated glycoproteins, S100Beta, heat shock protein alpha, beta crystallin, myelin-associated oligodendrocytic basic protein (MOBP), and 2′,3′ cyclic nucleotide 3′-phosphodiesterase.
 11. The process according to claim 4, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 6-32.
 12. The process according to claim 5, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from hsp60, hsp70, Ro60, La, SmD, and 70-kDa U1RNP.
 13. The process according to claim 5, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 92-140.
 14. The process according to claim 6, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from hsp60, glutamic acid decarboxylase (GAD65), insulinoma-antigen 2 (IA-2), and insulin.
 15. The process according to claim 6, wherein the amino acid sequence of the amino acid sequence of the epitope is selected from SEQ ID NOS: 44-91.
 16. The process according to claim 7, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from acetylcholine receptor (AChR) α-subunit and muscle-specific receptor tyrosine kinase (MuSK).
 17. The process according to claim 7, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 1-2.
 18. The process according to claim 8, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from type II collagen and hsp60.
 19. The process according to claim 8, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 3-5.
 20. The process according to claim 9, wherein the amino acid sequence of the epitope is a partial sequence of a protein selected from desmoglein 3 (Dsg3).
 21. The process according to claim 9, wherein the amino acid sequence of the epitope is selected from SEQ ID NOS: 33-43.
 22. The process according to claim 1, wherein the amino acid similarity is defined according to the similarity table shown in FIG.
 4. 23. The process of claim 1, wherein the conserved substitution is the most prevalent conserved substitution or a replacement defined according to amino acid similarity.
 24. A process for manufacturing a composition comprising directed sequence polymers (DSPs), comprising the steps of: (1) selecting a first base peptide sequence, wherein the sequence is an amino acid sequence of an epitope of an antigen associated with an autoimmune disease; (2) synthesizing by solid phase peptide synthesis a first cassette of the DSPs, each cassette having a sequence of amino acid positions corresponding to each amino acid of the base peptide sequence, wherein, for each amino acid position of the first cassette of the directed sequence polymers, an amino acid is added, said amino acid randomly selected from a mixture of amino acids comprising the original amino acid found at that amino acid position, alanine (A), and, optionally, at least one conserved substitution, wherein the amino acids in the mixture are present in a fixed molar input ratio relative to each other, determined prior to starting synthesis, wherein the relative molar amount of A is more than 10% and less than 90% of the total amino acid concentration of the DSPs; (3) optionally extending the length of the DSPs by at least one of: (a) repeating step (2) for 2 to 15 cycles and elongating the DSP under the same condition; or (b) repeating step (2) for 2 to 15 cycles and elongating the DSP, for each cycle, using a different input ratio of amino acids in the mixture; or (c) repeating steps (1) and (2) for 2 to 15 cycles and elongating the DSP using cassettes based on more than one base peptide; or (d) assembling 2 to 15 cassettes synthesized in a single cycle of step (2); or (e) assembling 2 to 15 cassettes, the first cassette synthesized under one condition of step (2), and second and more cassettes synthesized under other conditions of step (2); (4) optionally further elongating the DSPs by repeating steps (2) and (3) for 2 to 15 cycles, wherein for each cycle a new cassette of the DSP is designed independently from any of the previous cassettes designated by previous cycles of step (2); wherein the number of cycles selected in steps (3) and (4) is selected so that the final length of the DSP is about 25 to 300 amino acid residues. 